ABL2.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.69 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |2.14 |0 |
20 19
|DLBCL |No |No |0.00 |0 |
21 20
|FL |No |No |0.00 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ABL2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ABL2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ABL2_NM_007314.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ABL2.html)
7
+
8
+![image](../../images/proteinpaint/ABL2.svg)
ACAD9.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.358 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |5.352 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACAD9_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACAD9_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ACAD9_NM_014049.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACAD9.html)
7
+
8
+![image](../../images/proteinpaint/ACAD9.svg)
ACE.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |3.943 |0 |
22 21
|DLBCL |No |No |0.545 |0 |
23 22
|FL |No |No |1.256 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACE_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACE_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ACE_NM_000789.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACE.html)
7
+
8
+![image](../../images/proteinpaint/ACE.svg)
ACTB.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes | 8.60 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes | 9.18 |
15 14
|DLBCL |Schmitz cohort| 9.80 |
16 15
|DLBCL |Reddy cohort | 6.30 |
17 16
|DLBCL |Chapuy cohort |12.40 |
... ...
@@ -20,16 +19,24 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No | 5.217 |0 |
25 24
|DLBCL |Yes |No | 3.582 |0 |
26 25
|FL |Yes |No |10.476 |0 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
31
-|--------|----------|--------|------|------------------|
32
-|chr7 |5568297 |5570856 |TSS |active_promoter |
29
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
30
+|:--------:|:----------:|:--------:|:---------------------------------------------------------------------------------------:|:------------------:|
31
+|chr7 |5568297 |5570856 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr7%3A5568297%2D5570856)|active_promoter |
33 32
34 33
> [!NOTE]
35
-> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACTB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACTB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ACTB_NM_001101.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ACTB.html)
7
+
8
+![image](../../images/proteinpaint/ACTB.svg)
ACTG1.md
... ...
@@ -0,0 +1,34 @@
1
+# [ACTG1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene |
8
+|FL |2 |relevance in FL not firmly established|
9
+## Mutation incidence
10
+
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |5.35 |
14
+|DLBCL |Schmitz cohort| NA |
15
+|DLBCL |Reddy cohort | NA |
16
+|DLBCL |Chapuy cohort | NA |
17
+|FL |GAMBL genomes |3.00 |
18
+
19
+## Mutation pattern
20
+
21
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23
+|BL |Yes |No |2.063 |8.011 |
24
+|DLBCL |Yes |No |2.125 |0.000 |
25
+|FL |Yes |No |8.128 |0.000 |
26
+
27
+## aSHM regions
28
+
29
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
30
+|:--------:|:----------:|:--------:|:---------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr17 |79478289 |79479959|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A79478289%2D79479959)|NA |
32
+
33
+> [!NOTE]
34
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289). First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
ADAMTS1.md
... ...
@@ -0,0 +1,27 @@
1
+# [ADAMTS1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.907 |0.000 |
22
+|DLBCL |No |No |0.524 |7.778 |
23
+|FL |No |No |0.000 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
ADAMTS5.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.77 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.451 |5.235 |
22 21
|DLBCL |No |No |3.276 |0.000 |
23 22
|FL |No |No |2.666 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ADAMTS5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ADAMTS5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ADAMTS5_NM_007038.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ADAMTS5.html)
7
+
8
+![image](../../images/proteinpaint/ADAMTS5.svg)
ADNP.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.15 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.200 |17.917 |
22 21
|DLBCL |No |No |1.866 | 0.000 |
23 22
|FL |No |No |2.254 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ADNP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ADNP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ADNP_NM_015339.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ADNP.html)
7
+
8
+![image](../../images/proteinpaint/ADNP.svg)
AGO4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.15 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.183 | 0.000 |
22 21
|DLBCL |No |No |0.000 |11.202 |
23 22
|FL |No |No |0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AGO4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AGO4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/AGO4_NM_017629.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AGO4.html)
7
+
8
+![image](../../images/proteinpaint/AGO4.svg)
ALPK2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.93 |
14 13
|BL |Thomas cohort |5.10 |
15 14
|BL |Panea cohort |9.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.951 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |1.538 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ALPK2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ALPK2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ALPK2_NM_052947.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ALPK2.html)
7
+
8
+![image](../../images/proteinpaint/ALPK2.svg)
ANKRD12.md
... ...
@@ -0,0 +1,27 @@
1
+# [ANKRD12]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.649 |0.000 |
22
+|DLBCL |No |No |0.885 |4.832 |
23
+|FL |No |No |0.000 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
ANKRD17.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|4.3 |
15
-|DLBCL |Reddy cohort |3.8 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|4.30 |
14
+|DLBCL |Reddy cohort |3.80 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.047 |8.897 |
23 22
|DLBCL |No |No |1.492 |4.437 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD17_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD17_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ANKRD17_NM_032217.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD17.html)
7
+
8
+![image](../../images/proteinpaint/ANKRD17.svg)
ARHGEF1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.93 |
14 13
|BL |Thomas cohort |2.00 |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.954 |0.000 |
22 21
|DLBCL |No |No |2.662 |9.372 |
23 22
|FL |No |No |3.865 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307)
... ...
\ No newline at end of file
0
+> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARHGEF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARHGEF1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ARHGEF1_NM_199002.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARHGEF1.html)
7
+
8
+![image](../../images/proteinpaint/ARHGEF1.svg)
ARID1A.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|28.64 |
16 15
|BL |Thomas cohort |36.00 |
17 16
|BL |Panea cohort |19.80 |
18
-|DLBCL |GAMBL genomes | 8.40 |
17
+|DLBCL |GAMBL genomes | 8.80 |
19 18
|DLBCL |Schmitz cohort | 8.90 |
20 19
|DLBCL |Reddy cohort | 4.40 |
21 20
|DLBCL |Chapuy cohort | 4.30 |
... ...
@@ -23,12 +22,8 @@
23 22
24 23
## Mutation pattern
25 24
26
-[View BL in GenomePaint browser](https://proteinpaint.stjude.org/?position=chr1:27019726-27108595&block=on&genome=hg19&svcnvfpkmurl=GAMBL_BL,vcf,https://bcgsc.ca/downloads/morinlab/vsouza/bundled_allLymphomaGenes_genome_grch37/vcf/BL_sorted.vcf.gz)
27
-
28
-[View FL in GenomePaint browser](https://proteinpaint.stjude.org/?position=chr1:27019726-27108595&block=on&genome=hg19&svcnvfpkmurl=GAMBL_FL,vcf,https://bcgsc.ca/downloads/morinlab/vsouza/bundled_allLymphomaGenes_genome_grch37/vcf/FL_sorted.vcf.gz)
29
-
30 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
31
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
32 27
|BL |No |Yes |3.218 |130.201 |
33 28
|DLBCL |No |Yes |2.364 | 38.689 |
34 29
|FL |No |Yes |3.794 |248.722 |
... ...
@@ -36,3 +31,11 @@
36 31
37 32
> [!NOTE]
38 33
> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein_hg38.html)
36
+
37
+![image](../../images/proteinpaint/ARID1A_NM_006015.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A.html)
40
+
41
+![image](../../images/proteinpaint/ARID1A.svg)
ARID1B.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |5.0 |
14
-|DLBCL |Schmitz cohort|6.0 |
15
-|DLBCL |Reddy cohort |3.3 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |5.16 |
13
+|DLBCL |Schmitz cohort|6.00 |
14
+|DLBCL |Reddy cohort |3.30 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.659 | 4.236 |
23 22
|DLBCL |No |No |0.969 |13.782 |
24 23
|FL |No |No |0.747 |11.009 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ARID1B_NM_017519.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1B.html)
7
+
8
+![image](../../images/proteinpaint/ARID1B.svg)
ARID5B.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.6 |
14
-|DLBCL |Schmitz cohort|4.3 |
15
-|DLBCL |Reddy cohort |4.3 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.25 |
13
+|DLBCL |Schmitz cohort|4.30 |
14
+|DLBCL |Reddy cohort |4.30 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.378 |0 |
23 22
|DLBCL |No |No |2.263 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID5B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID5B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ARID5B_NM_032199.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID5B.html)
7
+
8
+![image](../../images/proteinpaint/ARID5B.svg)
ATM.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |5.2 |
14
-|DLBCL |Schmitz cohort|5.5 |
15
-|DLBCL |Reddy cohort |5.9 |
16
-|DLBCL |Chapuy cohort |4.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |6.88 |
13
+|DLBCL |Schmitz cohort|5.50 |
14
+|DLBCL |Reddy cohort |5.90 |
15
+|DLBCL |Chapuy cohort |4.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.461 |0.000 |
23 22
|DLBCL |No |No |3.529 |5.446 |
24 23
|FL |No |No |1.679 |6.201 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATM_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATM_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ATM_NM_000051.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATM.html)
7
+
8
+![image](../../images/proteinpaint/ATM.svg)
ATP2C2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.7 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.473 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |3.759 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP2C2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP2C2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ATP2C2_NM_014861.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP2C2.html)
7
+
8
+![image](../../images/proteinpaint/ATP2C2.svg)
ATP6AP1.md
... ...
@@ -2,21 +2,29 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|4.85 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No | 0.000 | 0.000 |
20 19
|DLBCL |No |No | 0.000 | 0.000 |
21 20
|FL |No |Yes |50.635 |72.487 |
22 21
22
+
23
+
24
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6AP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6AP1_protein_hg38.html)
25
+
26
+![image](../../images/proteinpaint/ATP6AP1_NM_001183.svg)
27
+
28
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6AP1.html)
29
+
30
+![image](../../images/proteinpaint/ATP6AP1.svg)
ATP6V1A.md
... ...
@@ -0,0 +1,24 @@
1
+# [ATP6V1A]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|1.15 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.321 |0 |
19
+|DLBCL |No |No |7.648 |0 |
20
+|FL |No |No |8.783 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
ATP6V1B2.md
... ...
@@ -2,21 +2,29 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|7.39 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No | 5.989 |0 |
20 19
|DLBCL |No |No | 1.297 |0 |
21 20
|FL |No |Yes |72.658 |0 |
22 21
22
+
23
+
24
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6V1B2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6V1B2_protein_hg38.html)
25
+
26
+![image](../../images/proteinpaint/ATP6V1B2_NM_001693.svg)
27
+
28
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6V1B2.html)
29
+
30
+![image](../../images/proteinpaint/ATP6V1B2.svg)
ATR.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|4.9 |
15
-|DLBCL |Reddy cohort |2.8 |
16
-|DLBCL |Chapuy cohort |3.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|4.90 |
14
+|DLBCL |Reddy cohort |2.80 |
15
+|DLBCL |Chapuy cohort |3.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.459 |0.000 |
23 22
|DLBCL |No |No |1.146 |3.261 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATR_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ATR_NM_001184.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATR.html)
7
+
8
+![image](../../images/proteinpaint/ATR.svg)
B2M.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 2.31 |
16 15
|BL |Thomas cohort | 2.50 |
17 16
|BL |Panea cohort | 3.00 |
18
-|DLBCL |GAMBL genomes |14.00 |
17
+|DLBCL |GAMBL genomes |15.11 |
19 18
|DLBCL |Schmitz cohort |15.50 |
20 19
|DLBCL |Reddy cohort |12.10 |
21 20
|DLBCL |Chapuy cohort |12.00 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 9.379 | 56.571 |
29 28
|DLBCL |No |Yes |60.843 |340.788 |
30 29
|FL |No |Yes |54.190 |326.834 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/B2M_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/B2M_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/B2M_NM_004048.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/B2M.html)
38
+
39
+![image](../../images/proteinpaint/B2M.svg)
BACH2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort |0.40 |
15 14
|BL |Panea cohort |5.00 |
... ...
@@ -17,16 +16,24 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |Yes |No |0.652 | 0.000 |
22 21
|DLBCL |Yes |No |0.949 | 0.000 |
23 22
|FL |Yes |No |0.000 |28.997 |
24 23
25 24
## aSHM regions
26 25
27
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
28
-|--------|----------|--------|------|------------------|
29
-|chr6 |90981034 |91016134|TSS |NA |
26
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
27
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
28
+|chr6 |90981034 |91016134|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134)|NA |
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BACH2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BACH2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BACH2_NM_021813.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BACH2.html)
7
+
8
+![image](../../images/proteinpaint/BACH2.svg)
BCL10.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|0.23 |
16 15
|BL |Thomas cohort |0.40 |
17 16
|BL |Panea cohort | NA |
18
-|DLBCL |GAMBL genomes |4.10 |
17
+|DLBCL |GAMBL genomes |3.82 |
19 18
|DLBCL |Schmitz cohort |7.70 |
20 19
|DLBCL |Reddy cohort |3.10 |
21 20
|DLBCL |Chapuy cohort |6.40 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 3.224 | 0.000 |
29 28
|DLBCL |No |Yes |13.754 |106.692 |
30 29
|FL |No |Yes | 0.000 |223.832 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL10_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/BCL10_NM_003921.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL10.html)
38
+
39
+![image](../../images/proteinpaint/BCL10.svg)
BCL11A.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|2.54 |
15 14
|BL |Thomas cohort |1.70 |
16 15
|BL |Panea cohort |5.90 |
17
-|DLBCL |GAMBL genomes |3.60 |
16
+|DLBCL |GAMBL genomes |4.02 |
18 17
|DLBCL |Schmitz cohort |4.50 |
19 18
|DLBCL |Reddy cohort |1.60 |
20 19
|DLBCL |Chapuy cohort |3.40 |
... ...
@@ -22,13 +21,22 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |No |4.455 | 0.000 |
27 26
|DLBCL |Yes |Yes |5.279 |69.578 |
28 27
|FL |Yes |No |1.180 | 0.000 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
33
-|--------|----------|--------|------|------------------|
34
-|chr2 |60773789 |60783486|TSS |active_promoter |
31
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
32
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
33
+|chr2 |60773789 |60783486|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A60773789%2D60783486)|active_promoter |
34
+
35
+
36
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL11A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL11A_protein_hg38.html)
37
+
38
+![image](../../images/proteinpaint/BCL11A_NM_022893.svg)
39
+
40
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL11A.html)
41
+
42
+![image](../../images/proteinpaint/BCL11A.svg)
BCL2.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 0.46 |
16 15
|BL |Thomas cohort | 0.00 |
17 16
|BL |Panea cohort | 1.00 |
18
-|DLBCL |GAMBL genomes |22.10 |
17
+|DLBCL |GAMBL genomes |23.71 |
19 18
|DLBCL |Schmitz cohort |10.60 |
20 19
|DLBCL |Reddy cohort |12.90 |
21 20
|DLBCL |Chapuy cohort |15.80 |
... ...
@@ -24,14 +23,23 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |0.000 |0 |
29 28
|DLBCL |Yes |Yes |2.645 |0 |
30 29
|FL |Yes |No |1.197 |0 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr18 |60796984 |60814103|intron|strong_enhancer |
37
-|chr18 |60982728 |60988342|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:---------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr18 |60796984 |60814103|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60796984%2D60814103)|strong_enhancer |
36
+|chr18 |60982728 |60988342|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342) |active_promoter |
37
+
38
+
39
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2_protein_hg38.html)
40
+
41
+![image](../../images/proteinpaint/BCL2_NM_000633.svg)
42
+
43
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2.html)
44
+
45
+![image](../../images/proteinpaint/BCL2.svg)
BCL2L11.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort |2.10 |
15 14
|BL |Panea cohort |1.00 |
... ...
@@ -17,13 +16,22 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |Yes |Yes |15.763 |114.229 |
22 21
|DLBCL |Yes |No | 5.483 | 0.000 |
23 22
|FL |Yes |No | 0.000 | 0.000 |
24 23
25 24
## aSHM regions
26 25
27
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
28
-|--------|----------|---------|------|------------------|
29
-|chr2 |111874854 |111882174|TSS |active_promoter |
26
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
27
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
28
+|chr2 |111874854 |111882174|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A111874854%2D111882174)|active_promoter |
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2L11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2L11_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/BCL2L11_NM_138621.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2L11.html)
36
+
37
+![image](../../images/proteinpaint/BCL2L11.svg)
BCL6.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 5.08 |
16 15
|BL |Thomas cohort | 3.40 |
17 16
|BL |Panea cohort | 7.90 |
18
-|DLBCL |GAMBL genomes |13.30 |
17
+|DLBCL |GAMBL genomes |11.66 |
19 18
|DLBCL |Schmitz cohort | 9.80 |
20 19
|DLBCL |Reddy cohort | 6.40 |
21 20
|DLBCL |Chapuy cohort | 5.10 |
... ...
@@ -24,21 +23,29 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 7.427 | 0.000 |
29 28
|DLBCL |Yes |Yes |25.672 |60.803 |
30 29
|FL |Yes |Yes |27.215 |62.162 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region |regulatory_comment|
35
-|--------|----------|---------|------------|------------------|
36
-|chr3 |187458526 |187464632|TSS |NA |
37
-|chr3 |187615533 |187625659|Intergenic-1|NA |
38
-|chr3 |187625659 |187638101|Intergenic-2|NA |
39
-|chr3 |187657518 |187665996|Intergenic-3|NA |
40
-|chr3 |187675741 |187690717|Intergenic-4|NA |
41
-|chr3 |187690717 |187705000|Intergenic-5|NA |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr3 |187458526 |187464632|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187458526%2D187464632) |NA |
36
+|chr3 |187615533 |187625659|[Intergenic-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187615533%2D187625659)|NA |
37
+|chr3 |187625659 |187638101|[Intergenic-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187625659%2D187638101)|NA |
38
+|chr3 |187657518 |187665996|[Intergenic-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187657518%2D187665996)|NA |
39
+|chr3 |187675741 |187690717|[Intergenic-4](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187675741%2D187690717)|NA |
40
+|chr3 |187690717 |187705000|[Intergenic-5](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187690717%2D187705000)|NA |
42 41
43 42
> [!NOTE]
44
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2023 by [Dreval K](https://pubmed.ncbi.nlm.nih.gov/37084389)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2023 by [Dreval K](https://pubmed.ncbi.nlm.nih.gov/37084389)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BCL6_NM_001706.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL6.html)
7
+
8
+![image](../../images/proteinpaint/BCL6.svg)
BCL7A.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 5.31 |
16 15
|BL |Thomas cohort | 5.50 |
17 16
|BL |Panea cohort | 5.00 |
18
-|DLBCL |GAMBL genomes | 8.80 |
17
+|DLBCL |GAMBL genomes | 7.65 |
19 18
|DLBCL |Schmitz cohort |10.60 |
20 19
|DLBCL |Reddy cohort | 8.40 |
21 20
|DLBCL |Chapuy cohort | 6.40 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |Yes | 9.127 | 46.248 |
29 28
|DLBCL |Yes |Yes |22.635 | 0.000 |
30 29
|FL |Yes |Yes |55.348 |146.110 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
35
-|--------|----------|---------|------|------------------|
36
-|chr12 |122456912 |122464036|TSS |poised_promoter |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr12 |122456912 |122464036|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A122456912%2D122464036)|poised_promoter |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL7A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL7A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BCL7A_NM_020993.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL7A.html)
7
+
8
+![image](../../images/proteinpaint/BCL7A.svg)
BCOR.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|7.7 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|7.70 |
14
+|DLBCL |Reddy cohort |2.50 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.341 |0 |
23 22
|DLBCL |No |No |2.471 |0 |
24 23
|FL |No |No |1.743 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCOR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCOR_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/BCOR_NM_017745.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCOR.html)
32
+
33
+![image](../../images/proteinpaint/BCOR.svg)
BCR.md
... ...
@@ -2,36 +2,43 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
14
-|BL |GAMBL genomes+capture| 6.0 |
15
-|BL |Thomas cohort | 6.4 |
16
-|BL |Panea cohort |10.9 |
17
-|DLBCL |GAMBL genomes | 4.5 |
18
-|DLBCL |Schmitz cohort | 6.4 |
19
-|DLBCL |Reddy cohort | 3.9 |
20
-|DLBCL |Chapuy cohort | 4.3 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture| 6.00 |
14
+|BL |Thomas cohort | 6.40 |
15
+|BL |Panea cohort |10.90 |
16
+|DLBCL |GAMBL genomes | 4.97 |
17
+|DLBCL |Schmitz cohort | 6.40 |
18
+|DLBCL |Reddy cohort | 3.90 |
19
+|DLBCL |Chapuy cohort | 4.30 |
21 20
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |No |2.733 |2.641 |
27 26
|DLBCL |Yes |No |1.249 |3.642 |
28 27
|FL |Yes |No |7.439 |0.000 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
33
-|--------|----------|--------|------|------------------|
34
-|chr22 |23522060 |23528313|TSS |NA |
31
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
32
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr22 |23522060 |23528313|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr22%3A23522060%2D23528313)|NA |
35 34
36 35
> [!NOTE]
37
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCR_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BCR_NM_004327.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCR.html)
7
+
8
+![image](../../images/proteinpaint/BCR.svg)
BIRC6.md
... ...
@@ -2,30 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
15
-|BL |GAMBL genomes+capture| 6.0 |
16
-|BL |Thomas cohort | 3.8 |
17
-|BL |Panea cohort |14.9 |
18
-|DLBCL |GAMBL genomes | 6.3 |
19
-|DLBCL |Schmitz cohort |10.0 |
20
-|DLBCL |Reddy cohort | 6.4 |
21
-|DLBCL |Chapuy cohort | 4.7 |
22
-|FL |GAMBL genomes | 3.7 |
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
14
+|BL |GAMBL genomes+capture| 6.00 |
15
+|BL |Thomas cohort | 3.80 |
16
+|BL |Panea cohort |14.90 |
17
+|DLBCL |GAMBL genomes | 7.27 |
18
+|DLBCL |Schmitz cohort |10.00 |
19
+|DLBCL |Reddy cohort | 6.40 |
20
+|DLBCL |Chapuy cohort | 4.70 |
21
+|FL |GAMBL genomes | 3.70 |
23 22
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |0.862 |1.339 |
29 28
|DLBCL |No |No |1.795 |5.011 |
30 29
|FL |No |No |2.997 |7.132 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC6_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/BIRC6_NM_016252.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC6.html)
38
+
39
+![image](../../images/proteinpaint/BIRC6.svg)
BMP7.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|BL |1 |high-confidence BL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|6.47 |
14 13
|BL |Thomas cohort |8.90 |
15 14
|BL |Panea cohort |5.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |Yes |5.863 |16.044 |
22 21
|DLBCL |No |No |6.236 |10.787 |
23 22
|FL |No |No |1.371 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BMP7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BMP7_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BMP7_NM_001719.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BMP7.html)
7
+
8
+![image](../../images/proteinpaint/BMP7.svg)
BRAF.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|2.77 |
15 14
|BL |Thomas cohort | NA |
16 15
|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |2.50 |
16
+|DLBCL |GAMBL genomes |2.29 |
18 17
|DLBCL |Schmitz cohort |3.40 |
19 18
|DLBCL |Reddy cohort |2.00 |
20 19
|DLBCL |Chapuy cohort |5.60 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |4.754 |0 |
27 26
|DLBCL |No |No |5.565 |0 |
28 27
|FL |No |No |4.680 |0 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRAF_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRAF_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BRAF_NM_004333.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRAF.html)
7
+
8
+![image](../../images/proteinpaint/BRAF.svg)
BRD4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.342 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRD4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRD4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BRD4_NM_058243.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRD4.html)
7
+
8
+![image](../../images/proteinpaint/BRD4.svg)
BRINP3.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |3.3 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |3.30 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |4.218 |0.00 |
23 22
|DLBCL |No |No |1.138 |0.00 |
24 23
|FL |No |No |1.586 |6.33 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRINP3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRINP3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BRINP3_NM_199051.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BRINP3.html)
7
+
8
+![image](../../images/proteinpaint/BRINP3.svg)
BTBD3.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|1.9 |
15
-|DLBCL |Reddy cohort |1.8 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Reddy cohort |1.80 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |5.604 |0 |
23 22
|DLBCL |No |No |0.722 |0 |
24 23
|FL |No |No |2.655 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTBD3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTBD3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BTBD3_NM_014962.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTBD3.html)
7
+
8
+![image](../../images/proteinpaint/BTBD3.svg)
BTG1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 0.46 |
16 15
|BL |Thomas cohort | NA |
17 16
|BL |Panea cohort | NA |
18
-|DLBCL |GAMBL genomes | 9.70 |
17
+|DLBCL |GAMBL genomes |10.13 |
19 18
|DLBCL |Schmitz cohort |14.50 |
20 19
|DLBCL |Reddy cohort | 7.50 |
21 20
|DLBCL |Chapuy cohort |14.50 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |0.000 |0.000 |
29 28
|DLBCL |Yes |No |0.498 |1.085 |
30 29
|FL |Yes |No |4.407 |6.147 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr12 |92537999 |92539598|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr12 |92537999 |92539598|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A92537999%2D92539598)|active_promoter |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTG1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTG1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BTG1_NM_001731.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTG1.html)
7
+
8
+![image](../../images/proteinpaint/BTG1.svg)
BTG2.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 4.85 |
16 15
|BL |Thomas cohort | 4.20 |
17 16
|BL |Panea cohort | 9.90 |
18
-|DLBCL |GAMBL genomes |14.00 |
17
+|DLBCL |GAMBL genomes |13.38 |
19 18
|DLBCL |Schmitz cohort |17.20 |
20 19
|DLBCL |Reddy cohort | 9.20 |
21 20
|DLBCL |Chapuy cohort | 6.00 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |6.152 |42.280 |
29 28
|DLBCL |Yes |Yes |3.562 |10.265 |
30 29
|FL |Yes |No |6.073 | 0.000 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
35
-|--------|----------|---------|------|------------------|
36
-|chr1 |203274698 |203275778|intron|active_promoter |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr1 |203274698 |203275778|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A203274698%2D203275778)|active_promoter |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTG2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTG2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/BTG2_NM_006763.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTG2.html)
7
+
8
+![image](../../images/proteinpaint/BTG2.svg)
BTK.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |5.40 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |6.88 |
15 14
|DLBCL |Schmitz cohort|3.60 |
16 15
|DLBCL |Reddy cohort |3.10 |
17 16
|DLBCL |Chapuy cohort |2.10 |
... ...
@@ -20,8 +19,17 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No | 0.964 | 8.202 |
25 24
|DLBCL |No |Yes |18.082 |28.027 |
26 25
|FL |No |Yes |39.808 |35.548 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTK_protein_hg38.html)
30
+
31
+![image](../../images/proteinpaint/BTK_NM_000061.svg)
32
+
33
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTK.html)
34
+
35
+![image](../../images/proteinpaint/BTK.svg)
C10orf12.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.46 |
14 13
|BL |Thomas cohort |0.00 |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,8 +16,15 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.452 |27.236 |
22 21
|DLBCL |No |Yes |1.140 |38.506 |
23 22
|FL |No |Yes |3.190 |81.421 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_protein_hg38.html)
27
+
28
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12.html)
29
+
30
+![image](../../images/proteinpaint/C10orf12.svg)
C6orf27.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,8 +16,14 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C6orf27_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C6orf27_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C6orf27.html)
5
+
6
+![image](../../images/proteinpaint/C6orf27.svg)
CAD.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.93 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.965 |0 |
22 21
|DLBCL |No |No |1.949 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CAD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CAD_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CAD_NM_004341.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CAD.html)
7
+
8
+![image](../../images/proteinpaint/CAD.svg)
CADPS2.md
... ...
@@ -0,0 +1,27 @@
1
+# [CADPS2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.63 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.311 |2.676 |
22
+|DLBCL |No |No |1.217 |1.199 |
23
+|FL |No |No |0.921 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
CARD11.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 4.16 |
16 15
|BL |Thomas cohort | 1.70 |
17 16
|BL |Panea cohort |10.90 |
18
-|DLBCL |GAMBL genomes | 9.90 |
17
+|DLBCL |GAMBL genomes |11.28 |
19 18
|DLBCL |Schmitz cohort |15.30 |
20 19
|DLBCL |Reddy cohort | 7.80 |
21 20
|DLBCL |Chapuy cohort | 8.10 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 5.307 | 0.000 |
29 28
|DLBCL |No |Yes |16.898 | 0.000 |
30 29
|FL |No |Yes |28.329 |27.096 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CARD11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CARD11_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/CARD11_NM_032415.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CARD11.html)
38
+
39
+![image](../../images/proteinpaint/CARD11.svg)
CARD4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,8 +16,14 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CARD4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CARD4_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CARD4.html)
5
+
6
+![image](../../images/proteinpaint/CARD4.svg)
CASP8.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|1.1 |
15
-|DLBCL |Reddy cohort |1.2 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|1.10 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |12.972 |0 |
23 22
|DLBCL |No |No | 6.371 |0 |
24 23
|FL |No |No | 8.788 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CASP8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CASP8_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CASP8_NM_001228.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CASP8.html)
7
+
8
+![image](../../images/proteinpaint/CASP8.svg)
CBLB.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.6 |
14
-|DLBCL |Schmitz cohort|2.8 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.72 |
13
+|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.956 |0 |
23 22
|DLBCL |No |No |2.519 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CBLB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CBLB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CBLB_NM_170662.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CBLB.html)
7
+
8
+![image](../../images/proteinpaint/CBLB.svg)
CCDC42BPB.md
... ...
@@ -0,0 +1,21 @@
1
+# [CCDC42BPB]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|NA |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+
19
+
20
+> [!NOTE]
21
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
CCL4.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | NA |
14
-|DLBCL |Schmitz cohort|1.5 |
15
-|DLBCL |Reddy cohort |0.6 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|1.50 |
14
+|DLBCL |Reddy cohort |0.60 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |3.891 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCL4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCL4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CCL4_NM_002984.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCL4.html)
7
+
8
+![image](../../images/proteinpaint/CCL4.svg)
CCND3.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|27.48 |
16 15
|BL |Thomas cohort |28.00 |
17 16
|BL |Panea cohort |17.80 |
18
-|DLBCL |GAMBL genomes | 6.80 |
17
+|DLBCL |GAMBL genomes | 7.46 |
19 18
|DLBCL |Schmitz cohort | 9.80 |
20 19
|DLBCL |Reddy cohort | 3.80 |
21 20
|DLBCL |Chapuy cohort | 4.70 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |97.799 |360.774 |
29 28
|DLBCL |No |Yes |19.557 | 60.833 |
30 29
|FL |No |No |24.611 | 0.000 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CCND3_NM_001760.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND3.html)
7
+
8
+![image](../../images/proteinpaint/CCND3.svg)
CCNF.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.194 |0 |
22 21
|DLBCL |No |No |1.303 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2015 by [Abate F](https://pubmed.ncbi.nlm.nih.gov/26468873)
... ...
\ No newline at end of file
0
+> First described in BL in 2015 by [Abate F](https://pubmed.ncbi.nlm.nih.gov/26468873)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCNF_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCNF_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CCNF_NM_001761.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCNF.html)
7
+
8
+![image](../../images/proteinpaint/CCNF.svg)
CCT6B.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.15 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.893 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCT6B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCT6B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CCT6B_NM_006584.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCT6B.html)
7
+
8
+![image](../../images/proteinpaint/CCT6B.svg)
CD22.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|1.7 |
15
-|DLBCL |Reddy cohort |2.8 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|1.70 |
14
+|DLBCL |Reddy cohort |2.80 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |4.287 |0 |
23 22
|DLBCL |No |No |1.951 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD22_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD22_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CD22_NM_001771.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD22.html)
7
+
8
+![image](../../images/proteinpaint/CD22.svg)
CD274.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|2.3 |
15
-|DLBCL |Reddy cohort |1.3 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|2.30 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |5.538 | 0.000 |
23 22
|DLBCL |No |No |2.633 |49.045 |
24 23
|FL |No |No |4.631 |42.709 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD274_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD274_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CD274_NM_014143.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD274.html)
7
+
8
+![image](../../images/proteinpaint/CD274.svg)
CD36.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|4.9 |
15
-|DLBCL |Reddy cohort |2.8 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|4.90 |
14
+|DLBCL |Reddy cohort |2.80 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |4.616 |0.000 |
23 22
|DLBCL |No |No |0.822 |7.247 |
24 23
|FL |No |No |1.559 |0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD36_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD36_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/CD36_NM_001001548.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD36.html)
32
+
33
+![image](../../images/proteinpaint/CD36.svg)
CD58.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 0.92 |
15 14
|BL |Thomas cohort | 0.80 |
16 15
|BL |Panea cohort | 2.00 |
17
-|DLBCL |GAMBL genomes | 8.40 |
16
+|DLBCL |GAMBL genomes | 7.84 |
18 17
|DLBCL |Schmitz cohort |10.00 |
19 18
|DLBCL |Reddy cohort | 2.80 |
20 19
|DLBCL |Chapuy cohort | 6.80 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |3.10 | 32.536 |
27 26
|DLBCL |No |Yes |8.62 |292.453 |
28 27
|FL |No |Yes |0.00 |107.458 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/CD58_NM_001779.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58.html)
36
+
37
+![image](../../images/proteinpaint/CD58.svg)
CD70.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|0.92 |
16 15
|BL |Thomas cohort |0.40 |
17 16
|BL |Panea cohort |3.00 |
18
-|DLBCL |GAMBL genomes |5.60 |
17
+|DLBCL |GAMBL genomes |5.54 |
19 18
|DLBCL |Schmitz cohort |9.40 |
20 19
|DLBCL |Reddy cohort |6.90 |
21 20
|DLBCL |Chapuy cohort |7.70 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 2.199 | 0.000 |
29 28
|DLBCL |No |Yes |28.493 |249.836 |
30 29
|FL |No |No | 0.000 |106.251 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD70_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD70_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/CD70_NM_001252.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD70.html)
38
+
39
+![image](../../images/proteinpaint/CD70.svg)
CD79A.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.23 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 | 0.000 |
22 21
|DLBCL |No |No |1.810 |16.146 |
23 22
|FL |No |No |3.676 |33.801 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD79A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD79A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CD79A_NM_001783.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD79A.html)
7
+
8
+![image](../../images/proteinpaint/CD79A.svg)
CD79B.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 1.39 |
16 15
|BL |Thomas cohort | 0.00 |
17 16
|BL |Panea cohort | 4.00 |
18
-|DLBCL |GAMBL genomes | 9.50 |
17
+|DLBCL |GAMBL genomes | 9.94 |
19 18
|DLBCL |Schmitz cohort |14.90 |
20 19
|DLBCL |Reddy cohort | 8.30 |
21 20
|DLBCL |Chapuy cohort |15.40 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 0.000 | 0.000 |
29 28
|DLBCL |No |Yes |16.616 |41.932 |
30 29
|FL |No |No |10.310 | 0.000 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD79B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD79B_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/CD79B_NM_000626.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD79B.html)
38
+
39
+![image](../../images/proteinpaint/CD79B.svg)
CD83.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|1.15 |
16 15
|BL |Thomas cohort |1.70 |
17 16
|BL |Panea cohort | NA |
18
-|DLBCL |GAMBL genomes |4.50 |
17
+|DLBCL |GAMBL genomes |4.40 |
19 18
|DLBCL |Schmitz cohort |5.70 |
20 19
|DLBCL |Reddy cohort |5.80 |
21 20
|DLBCL |Chapuy cohort |7.30 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |4.396 | 0.000 |
29 28
|DLBCL |Yes |No |4.794 |14.227 |
30 29
|FL |Yes |No |0.000 |25.732 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment |
35
-|--------|----------|--------|------|-------------------------------|
36
-|chr6 |14118026 |14120025|TSS |active_promoter-strong_enhancer|
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment |
34
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:-------------------------------:|
35
+|chr6 |14118026 |14120025|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A14118026%2D14120025)|active_promoter-strong_enhancer|
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD83_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD83_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CD83_NM_004233.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD83.html)
7
+
8
+![image](../../images/proteinpaint/CD83.svg)
CDC73.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|2.54 |
15 14
|BL |Thomas cohort | NA |
16 15
|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |0.70 |
16
+|DLBCL |GAMBL genomes |0.57 |
18 17
|DLBCL |Schmitz cohort |0.60 |
19 18
|DLBCL |Reddy cohort |0.70 |
20 19
|DLBCL |Chapuy cohort |1.30 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |3.951 |0 |
27 26
|DLBCL |No |No |1.702 |0 |
28 27
|FL |No |No |3.603 |0 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDC73_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDC73_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CDC73_NM_024529.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDC73.html)
7
+
8
+![image](../../images/proteinpaint/CDC73.svg)
CDH17.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 |0.000 |
22 21
|DLBCL |No |No |0.635 |6.343 |
23 22
|FL |No |No |0.000 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH17_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH17_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CDH17_NM_004063.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH17.html)
7
+
8
+![image](../../images/proteinpaint/CDH17.svg)
CDKN2A.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|1.85 |
15 14
|BL |Thomas cohort |3.00 |
16 15
|BL |Panea cohort |3.00 |
17
-|DLBCL |GAMBL genomes |2.90 |
16
+|DLBCL |GAMBL genomes |3.25 |
18 17
|DLBCL |Schmitz cohort |6.00 |
19 18
|DLBCL |Reddy cohort |1.00 |
20 19
|DLBCL |Chapuy cohort |1.70 |
... ...
@@ -22,5 +21,14 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
25
+
26
+
27
+
28
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2A_protein_hg38.html)
29
+
30
+![image](../../images/proteinpaint/CDKN2A_NM_000077.svg)
31
+
32
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2A.html)
26 33
34
+![image](../../images/proteinpaint/CDKN2A.svg)
CDKN2C.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.54 |
14 13
|BL |Thomas cohort |3.40 |
15 14
|BL |Panea cohort |3.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |16.525 |50.872 |
22 21
|DLBCL |No |No | 3.474 | 0.000 |
23 22
|FL |No |No | 0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743)
... ...
\ No newline at end of file
0
+> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2C_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CDKN2C_NM_001262.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2C.html)
7
+
8
+![image](../../images/proteinpaint/CDKN2C.svg)
CHD1.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|3.0 |
15 14
|DLBCL |Reddy cohort |2.9 |
16 15
|DLBCL |Chapuy cohort |2.1 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.674 |2.751 |
23 22
|DLBCL |No |No |1.993 |4.965 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CHD1_NM_001270.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD1.html)
7
+
8
+![image](../../images/proteinpaint/CHD1.svg)
CHD4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.93 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.781 |0 |
22 21
|DLBCL |No |No |3.513 |0 |
23 22
|FL |No |No |1.815 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CHD4_NM_001273.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD4.html)
7
+
8
+![image](../../images/proteinpaint/CHD4.svg)
CHD8.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 8.78 |
15 14
|BL |Thomas cohort | 8.50 |
16 15
|BL |Panea cohort |16.80 |
17
-|DLBCL |GAMBL genomes | 1.80 |
16
+|DLBCL |GAMBL genomes | 1.91 |
18 17
|DLBCL |Schmitz cohort | 3.60 |
19 18
|DLBCL |Reddy cohort | 2.90 |
20 19
|DLBCL |Chapuy cohort | 3.00 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |3.551 |14.940 |
27 26
|DLBCL |No |No |1.619 | 0.000 |
28 27
|FL |No |No |1.344 |12.679 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD8_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CHD8_NM_001170629.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHD8.html)
7
+
8
+![image](../../images/proteinpaint/CHD8.svg)
CHST2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|2.3 |
15
-|DLBCL |Reddy cohort |0.7 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|2.30 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.786 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHST2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHST2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CHST2_NM_004267.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CHST2.html)
7
+
8
+![image](../../images/proteinpaint/CHST2.svg)
CIITA.md
... ...
@@ -2,32 +2,39 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|6.6 |
15
-|DLBCL |Reddy cohort |4.3 |
16
-|DLBCL |Chapuy cohort |4.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.87 |
13
+|DLBCL |Schmitz cohort|6.60 |
14
+|DLBCL |Reddy cohort |4.30 |
15
+|DLBCL |Chapuy cohort |4.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |1.029 |0.000 |
23 22
|DLBCL |Yes |No |0.648 |4.031 |
24 23
|FL |Yes |No |2.701 |0.000 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment |
29
-|--------|----------|--------|------|-------------------------------|
30
-|chr16 |10970795 |10975465|TSS |active_promoter-strong_enhancer|
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment |
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:-------------------------------:|
29
+|chr16 |10970795 |10975465|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A10970795%2D10975465)|active_promoter-strong_enhancer|
31 30
32 31
> [!NOTE]
33
-> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CIITA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CIITA_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CIITA_NM_000246.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CIITA.html)
7
+
8
+![image](../../images/proteinpaint/CIITA.svg)
CILP.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.46 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.915 |0 |
20 19
|DLBCL |No |No |0.460 |0 |
21 20
|FL |No |No |0.000 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CILP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CILP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CILP_NM_003613.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CILP.html)
7
+
8
+![image](../../images/proteinpaint/CILP.svg)
CNOT2.md
... ...
@@ -0,0 +1,27 @@
1
+# [CNOT2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.053 | 0.000 |
22
+|DLBCL |No |No |5.016 |12.509 |
23
+|FL |No |No |0.000 |23.991 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
COL4A2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.16 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.564 |0 |
22 21
|DLBCL |No |No |1.209 |0 |
23 22
|FL |No |No |1.043 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL4A2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL4A2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/COL4A2_NM_001846.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL4A2.html)
7
+
8
+![image](../../images/proteinpaint/COL4A2.svg)
COQ7.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.2 |
14
-|DLBCL |Schmitz cohort|0.6 |
15
-|DLBCL |Reddy cohort |0.5 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|0.60 |
14
+|DLBCL |Reddy cohort |0.50 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.304 |0 |
23 22
|DLBCL |No |No |2.025 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COQ7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COQ7_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/COQ7_NM_016138.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COQ7.html)
7
+
8
+![image](../../images/proteinpaint/COQ7.svg)
CPNE8.md
... ...
@@ -0,0 +1,24 @@
1
+# [CPNE8]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|2.08 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.932 | 0.000 |
19
+|DLBCL |No |No |2.398 | 0.000 |
20
+|FL |No |No |1.808 |12.601 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
CPXM2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.570 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |1.307 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CPXM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CPXM2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CPXM2_NM_198148.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CPXM2.html)
7
+
8
+![image](../../images/proteinpaint/CPXM2.svg)
CREBBP.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 6.00 |
16 15
|BL |Thomas cohort | 3.00 |
17 16
|BL |Panea cohort |12.90 |
18
-|DLBCL |GAMBL genomes |21.40 |
17
+|DLBCL |GAMBL genomes |25.81 |
19 18
|DLBCL |Schmitz cohort |17.90 |
20 19
|DLBCL |Reddy cohort |12.10 |
21 20
|DLBCL |Chapuy cohort |16.70 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 1.357 | 3.999 |
29 28
|DLBCL |No |Yes |13.231 | 65.302 |
30 29
|FL |No |Yes |43.869 |112.938 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CREBBP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CREBBP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CREBBP_NM_004380.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CREBBP.html)
7
+
8
+![image](../../images/proteinpaint/CREBBP.svg)
CRIP1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.2 |
14
-|DLBCL |Schmitz cohort|1.9 |
15
-|DLBCL |Reddy cohort |0.7 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |4.617 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CRIP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CRIP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CRIP1_NM_001311.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CRIP1.html)
7
+
8
+![image](../../images/proteinpaint/CRIP1.svg)
CTCF.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.0 |
14 13
|BL |Thomas cohort |1.7 |
15 14
|BL |Panea cohort |6.9 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |5.383 |0 |
22 21
|DLBCL |No |No |4.542 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTCF_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTCF_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CTCF_NM_006565.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTCF.html)
7
+
8
+![image](../../images/proteinpaint/CTCF.svg)
CTSS.md
... ...
@@ -2,21 +2,29 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|3.93 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No | 0.000 | 0.000 |
20 19
|DLBCL |No |No | 2.851 | 0.000 |
21 20
|FL |No |Yes |71.282 |54.511 |
22 21
22
+
23
+
24
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTSS_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTSS_protein_hg38.html)
25
+
26
+![image](../../images/proteinpaint/CTSS_NM_004079.svg)
27
+
28
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTSS.html)
29
+
30
+![image](../../images/proteinpaint/CTSS.svg)
CXCR4.md
... ...
@@ -2,36 +2,45 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
10 10
## Mutation incidence
11 11
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
14 14
|BL |GAMBL genomes+capture|2.08 |
15 15
|BL |Thomas cohort |2.10 |
16 16
|BL |Panea cohort |2.00 |
17
-|DLBCL |GAMBL genomes |2.70 |
17
+|DLBCL |GAMBL genomes |2.87 |
18 18
|DLBCL |Schmitz cohort |2.60 |
19 19
|DLBCL |Reddy cohort |1.50 |
20 20
|DLBCL |Chapuy cohort |2.60 |
21
+|FL |GAMBL genomes |3.46 |
21 22
22 23
## Mutation pattern
23 24
24 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 27
|BL |Yes |No |4.603 | 0.000 |
27 28
|DLBCL |Yes |No |3.731 |18.727 |
28 29
|FL |Yes |No |0.000 | 0.000 |
29 30
30 31
## aSHM regions
31 32
32
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
33
-|--------|----------|---------|------|------------------|
34
-|chr2 |136874728 |136875461|intron|weak_promoter |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr2 |136874728 |136875461|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A136874728%2D136875461)|weak_promoter |
35 36
36 37
> [!NOTE]
37
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2012 by [Khodabakhshi AH](https://pubmed.ncbi.nlm.nih.gov/23131835)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2012 by [Khodabakhshi AH](https://pubmed.ncbi.nlm.nih.gov/23131835). First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CXCR4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CXCR4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CXCR4_NM_001008540.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CXCR4.html)
7
+
8
+![image](../../images/proteinpaint/CXCR4.svg)
CXCR5.md
... ...
@@ -2,32 +2,39 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|4.0 |
15
-|DLBCL |Reddy cohort |2.1 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort|4.00 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |2.351 | 0.000 |
23 22
|DLBCL |Yes |No |1.785 | 0.000 |
24 23
|FL |Yes |No |2.934 |76.955 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
29
-|--------|----------|---------|------|------------------|
30
-|chr11 |118754458 |118756514|TSS |NA |
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr11 |118754458 |118756514|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A118754458%2D118756514)|NA |
31 30
32 31
> [!NOTE]
33
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CXCR5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CXCR5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CXCR5_NM_001716.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CXCR5.html)
7
+
8
+![image](../../images/proteinpaint/CXCR5.svg)
CYB5D1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.23 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0 |0 |
22 21
|DLBCL |No |No |0 |0 |
23 22
|FL |No |No |0 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYB5D1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYB5D1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CYB5D1_NM_144607.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYB5D1.html)
7
+
8
+![image](../../images/proteinpaint/CYB5D1.svg)
CYP2A6.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.23 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.079 |0 |
20 19
|DLBCL |No |No |0.000 |0 |
21 20
|FL |No |No |0.000 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYP2A6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYP2A6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CYP2A6_NM_000762.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYP2A6.html)
7
+
8
+![image](../../images/proteinpaint/CYP2A6.svg)
CYP4F22.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.467 |9.614 |
22 21
|DLBCL |No |No |1.320 |0.000 |
23 22
|FL |No |No |0.000 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYP4F22_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYP4F22_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/CYP4F22_NM_173483.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CYP4F22.html)
7
+
8
+![image](../../images/proteinpaint/CYP4F22.svg)
DAZAP1.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
14
-|DLBCL |Schmitz cohort|5.3 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort|5.30 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 | 0.000 |
23 22
|DLBCL |No |No |0 |35.642 |
24 23
|FL |No |No |0 |53.351 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DAZAP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DAZAP1_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/DAZAP1_ENST00000233078.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DAZAP1.html)
32
+
33
+![image](../../images/proteinpaint/DAZAP1.svg)
DCAF6.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|2.3 |
15
-|DLBCL |Reddy cohort |1.3 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|2.30 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.969 |0 |
23 22
|DLBCL |No |No |3.355 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DCAF6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DCAF6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DCAF6_NM_018442.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DCAF6.html)
7
+
8
+![image](../../images/proteinpaint/DCAF6.svg)
DDX10.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|1.5 |
15
-|DLBCL |Reddy cohort |0.8 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|1.50 |
14
+|DLBCL |Reddy cohort |0.80 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.927 |0.000 |
23 22
|DLBCL |No |No |0.000 |7.884 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DDX10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DDX10_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DDX10_NM_004398.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DDX10.html)
7
+
8
+![image](../../images/proteinpaint/DDX10.svg)
DDX3X.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|44.34 |
16 15
|BL |Thomas cohort |48.70 |
17 16
|BL |Panea cohort |39.60 |
18
-|DLBCL |GAMBL genomes | 8.60 |
17
+|DLBCL |GAMBL genomes | 8.80 |
19 18
|DLBCL |Schmitz cohort | 4.70 |
20 19
|DLBCL |Reddy cohort | 4.50 |
21 20
|DLBCL |Chapuy cohort | 5.60 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |Yes |19.270 |125.826 |
29 28
|DLBCL |Yes |No | 3.193 | 8.744 |
30 29
|FL |Yes |No |11.136 | 21.489 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region |regulatory_comment|
35
-|--------|----------|--------|----------|------------------|
36
-|chrX |42800580 |42804184|intergenic|NA |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------------:|:------------------:|
35
+|chrX |42800580 |42804184|[intergenic](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A42800580%2D42804184)|NA |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966). First described in FL in 2023 by [Dreval K](https://pubmed.ncbi.nlm.nih.gov/37084389)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966). First described in FL in 2023 by [Dreval K](https://pubmed.ncbi.nlm.nih.gov/37084389)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DDX3X_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DDX3X_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DDX3X_NM_001356.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DDX3X.html)
7
+
8
+![image](../../images/proteinpaint/DDX3X.svg)
DHX15.md
... ...
@@ -0,0 +1,24 @@
1
+# [DHX15]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|0.69 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.721 | 0.000 |
19
+|DLBCL |No |No |0.742 | 0.000 |
20
+|FL |No |No |2.763 |23.133 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
DHX16.md
... ...
@@ -0,0 +1,27 @@
1
+# [DHX16]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.298 | 0.00 |
22
+|DLBCL |No |No |2.652 |11.87 |
23
+|FL |No |No |3.825 | 0.00 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
DICER1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|2.3 |
15
-|DLBCL |Reddy cohort |1.1 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|2.30 |
14
+|DLBCL |Reddy cohort |1.10 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.609 |0 |
23 22
|DLBCL |No |No |0.818 |0 |
24 23
|FL |No |No |2.448 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DICER1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DICER1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DICER1_NM_177438.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DICER1.html)
7
+
8
+![image](../../images/proteinpaint/DICER1.svg)
DLGAP1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.501 |0 |
22 21
|DLBCL |No |No |1.143 |0 |
23 22
|FL |No |No |0.682 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLGAP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLGAP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DLGAP1_NM_004746.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLGAP1.html)
7
+
8
+![image](../../images/proteinpaint/DLGAP1.svg)
DNM2.md
... ...
@@ -0,0 +1,27 @@
1
+# [DNM2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No | 1.878 |7.821 |
22
+|DLBCL |No |No | 4.605 |0.000 |
23
+|FL |No |No |10.522 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
DNMT1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort |1.70 |
15 14
|BL |Panea cohort |5.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.947 |0.000 |
22 21
|DLBCL |No |No |0.000 |6.494 |
23 22
|FL |No |No |2.053 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNMT1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNMT1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DNMT1_NM_001130823.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNMT1.html)
7
+
8
+![image](../../images/proteinpaint/DNMT1.svg)
DNMT3A.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|2.1 |
15
-|DLBCL |Reddy cohort |1.4 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.76 |
13
+|DLBCL |Schmitz cohort|2.10 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 |0 |
23 22
|DLBCL |No |No |0 |0 |
24 23
|FL |No |No |0 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNMT3A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNMT3A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DNMT3A_NM_175629.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNMT3A.html)
7
+
8
+![image](../../images/proteinpaint/DNMT3A.svg)
DOCK1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | 3.8 |
14
-|DLBCL |Schmitz cohort|10.2 |
15
-|DLBCL |Reddy cohort | 4.9 |
16
-|DLBCL |Chapuy cohort | 6.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 3.82 |
13
+|DLBCL |Schmitz cohort|10.20 |
14
+|DLBCL |Reddy cohort | 4.90 |
15
+|DLBCL |Chapuy cohort | 6.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.528 |0 |
23 22
|DLBCL |No |No |1.001 |0 |
24 23
|FL |No |No |1.838 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DOCK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DOCK1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DOCK1_NM_001380.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DOCK1.html)
7
+
8
+![image](../../images/proteinpaint/DOCK1.svg)
DTX1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 5.54 |
16 15
|BL |Thomas cohort | 5.90 |
17 16
|BL |Panea cohort | 8.90 |
18
-|DLBCL |GAMBL genomes |10.20 |
17
+|DLBCL |GAMBL genomes |10.71 |
19 18
|DLBCL |Schmitz cohort |13.60 |
20 19
|DLBCL |Reddy cohort | 5.90 |
21 20
|DLBCL |Chapuy cohort |11.50 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |5.556 |14.253 |
29 28
|DLBCL |Yes |Yes |2.228 | 4.244 |
30 29
|FL |Yes |No |6.305 | 0.000 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
35
-|--------|----------|---------|------|------------------|
36
-|chr12 |113492311 |113497546|TSS |NA |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr12 |113492311 |113497546|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A113492311%2D113497546)|NA |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DTX1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DTX1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DTX1_NM_004416.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DTX1.html)
7
+
8
+![image](../../images/proteinpaint/DTX1.svg)
DUSP2.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene |
8
+|FL |2 |relevance in FL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes | 9.30 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |10.13 |
15 14
|DLBCL |Schmitz cohort|12.60 |
16 15
|DLBCL |Reddy cohort | 9.70 |
17 16
|DLBCL |Chapuy cohort | 4.30 |
... ...
@@ -20,16 +19,24 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No |1.258 |17.913 |
25 24
|DLBCL |Yes |No |1.537 |12.012 |
26 25
|FL |Yes |No |3.206 | 0.000 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end|region |regulatory_comment|
31
-|--------|----------|--------|--------|------------------|
32
-|chr2 |96808901 |96811913|intron-1|enhancer |
29
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
30
+|:--------:|:----------:|:--------:|:----------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr2 |96808901 |96811913|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A96808901%2D96811913)|enhancer |
33 32
34 33
> [!NOTE]
35
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DUSP2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DUSP2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/DUSP2_NM_004418.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DUSP2.html)
7
+
8
+![image](../../images/proteinpaint/DUSP2.svg)
E2F2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |7.419 |25.977 |
22 21
|DLBCL |No |No |0.000 | 0.000 |
23 22
|FL |No |No |0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/E2F2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/E2F2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/E2F2_NM_004091.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/E2F2.html)
7
+
8
+![image](../../images/proteinpaint/E2F2.svg)
EBF1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 2.08 |
16 15
|BL |Thomas cohort | 1.30 |
17 16
|BL |Panea cohort | 5.90 |
18
-|DLBCL |GAMBL genomes | 8.80 |
17
+|DLBCL |GAMBL genomes | 8.99 |
19 18
|DLBCL |Schmitz cohort |10.90 |
20 19
|DLBCL |Reddy cohort | 8.80 |
21 20
|DLBCL |Chapuy cohort |12.80 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 2.304 | 0.000 |
29 28
|DLBCL |Yes |Yes |11.910 |66.114 |
30 29
|FL |Yes |Yes |17.826 |91.742 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
35
-|--------|----------|---------|------|------------------|
36
-|chr5 |158500476 |158532769|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr5 |158500476 |158532769|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A158500476%2D158532769)|active_promoter |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EBF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EBF1_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/EBF1_NM_024007.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EBF1.html)
43
+
44
+![image](../../images/proteinpaint/EBF1.svg)
EDNRB.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |3.877 | 0.000 |
22 21
|DLBCL |No |No |0.482 | 0.000 |
23 22
|FL |No |No |2.521 |28.057 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EDNRB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EDNRB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EDNRB_NM_000115.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EDNRB.html)
7
+
8
+![image](../../images/proteinpaint/EDNRB.svg)
EEF1A1.md
... ...
@@ -2,27 +2,36 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene |
8
+|FL |2 |relevance in FL not firmly established|
9 9
## Mutation incidence
10 10
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.1 |
14
-|DLBCL |Schmitz cohort|3.0 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |4.7 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes | 4.78 |
14
+|DLBCL |Schmitz cohort| 3.00 |
15
+|DLBCL |Reddy cohort | 2.50 |
16
+|DLBCL |Chapuy cohort | 4.70 |
17
+|FL |GAMBL genomes |11.32 |
17 18
18 19
## Mutation pattern
19 20
20 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 23
|BL |No |No | 6.692 | 0.000 |
23 24
|DLBCL |No |No | 3.556 |24.091 |
24 25
|FL |No |Yes |47.451 | 0.000 |
25 26
26 27
27 28
> [!NOTE]
28
-> First described in DLBCL in 2021 by [Mosquera Orgueira A](https://pubmed.ncbi.nlm.nih.gov/33945543)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2021 by [Mosquera Orgueira A](https://pubmed.ncbi.nlm.nih.gov/33945543). First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EEF1A1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EEF1A1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EEF1A1_NM_001402.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EEF1A1.html)
7
+
8
+![image](../../images/proteinpaint/EEF1A1.svg)
EHD1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort |0.00 |
15 14
|BL |Panea cohort |5.90 |
... ...
@@ -17,8 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 | 0.000 |
22 21
|DLBCL |No |No |2.422 |16.476 |
23 22
|FL |No |No |2.540 | 0.000 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EHD1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EHD1_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/EHD1_NM_006795.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EHD1.html)
31
+
32
+![image](../../images/proteinpaint/EHD1.svg)
EIF2C4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,8 +16,14 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2C4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2C4_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2C4.html)
5
+
6
+![image](../../images/proteinpaint/EIF2C4.svg)
EIF4A1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|BL |1 |high-confidence BL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.85 |
14 13
|BL |Thomas cohort |5.10 |
15 14
|BL |Panea cohort |6.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |8.506 |0 |
22 21
|DLBCL |No |No |2.745 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF4A1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF4A1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EIF4A1_NM_001416.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF4A1.html)
7
+
8
+![image](../../images/proteinpaint/EIF4A1.svg)
EML2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |3.717 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EML2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EML2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EML2_NM_012155.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EML2.html)
7
+
8
+![image](../../images/proteinpaint/EML2.svg)
ENTPD3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.892 |16.794 |
22 21
|DLBCL |No |No |1.331 | 0.000 |
23 22
|FL |No |No |0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ENTPD3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ENTPD3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ENTPD3_NM_001248.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ENTPD3.html)
7
+
8
+![image](../../images/proteinpaint/ENTPD3.svg)
EP300.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 4.62 |
16 15
|BL |Thomas cohort | 4.20 |
17 16
|BL |Panea cohort | 7.90 |
18
-|DLBCL |GAMBL genomes | 9.50 |
17
+|DLBCL |GAMBL genomes |11.85 |
19 18
|DLBCL |Schmitz cohort | 9.80 |
20 19
|DLBCL |Reddy cohort | 7.10 |
21 20
|DLBCL |Chapuy cohort | 8.10 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 2.769 |3.550 |
29 28
|DLBCL |No |No | 3.344 |7.980 |
30 29
|FL |No |Yes |15.586 |7.719 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EP300_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EP300_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/EP300_NM_001429.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EP300.html)
38
+
39
+![image](../../images/proteinpaint/EP300.svg)
EPHB2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.886 |0 |
22 21
|DLBCL |No |No |0.586 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EPHB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EPHB2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EPHB2_NM_017449.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EPHB2.html)
7
+
8
+![image](../../images/proteinpaint/EPHB2.svg)
EPPK1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|BL |1 |high-confidence BL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture| 6.47 |
14 13
|BL |Thomas cohort | 7.60 |
15 14
|BL |Panea cohort |15.80 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.066 |0.0 |
22 21
|DLBCL |No |No |1.164 |7.7 |
23 22
|FL |No |No |2.802 |0.0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EPPK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EPPK1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EPPK1_NM_031308.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EPPK1.html)
7
+
8
+![image](../../images/proteinpaint/EPPK1.svg)
ERAP1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |3.083 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ERAP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ERAP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ERAP1_NM_016442.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ERAP1.html)
7
+
8
+![image](../../images/proteinpaint/ERAP1.svg)
ETS1.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 7.62 |
15 14
|BL |Thomas cohort | 7.60 |
16 15
|BL |Panea cohort |11.90 |
17
-|DLBCL |GAMBL genomes | 5.40 |
16
+|DLBCL |GAMBL genomes | 4.59 |
18 17
|DLBCL |Schmitz cohort | 7.90 |
19 18
|DLBCL |Reddy cohort | 4.40 |
20 19
|DLBCL |Chapuy cohort | 5.60 |
... ...
@@ -22,17 +21,25 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |No |5.097 |18.417 |
27 26
|DLBCL |Yes |No |2.987 | 0.000 |
28 27
|FL |Yes |No |5.163 |25.463 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
33
-|--------|----------|---------|------|------------------|
34
-|chr11 |128339774 |128345731|intron|enhancer |
35
-|chr11 |128388492 |128394163|TSS-2 |active_promoter |
31
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
32
+|:--------:|:----------:|:---------:|:-----------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr11 |128339774 |128345731|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A128339774%2D128345731)|enhancer |
34
+|chr11 |128388492 |128394163|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A128388492%2D128394163) |active_promoter |
36 35
37 36
> [!NOTE]
38
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ETS1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ETS1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ETS1_NM_001143820.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ETS1.html)
7
+
8
+![image](../../images/proteinpaint/ETS1.svg)
ETV6.md
... ...
@@ -2,29 +2,37 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | 5.6 |
14
-|DLBCL |Schmitz cohort|10.4 |
15
-|DLBCL |Reddy cohort | 5.8 |
16
-|DLBCL |Chapuy cohort |10.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 4.97 |
13
+|DLBCL |Schmitz cohort|10.40 |
14
+|DLBCL |Reddy cohort | 5.80 |
15
+|DLBCL |Chapuy cohort |10.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |1.527 | 0.000 |
23 22
|DLBCL |Yes |Yes |2.366 |28.723 |
24 23
|FL |Yes |No |2.772 | 0.000 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr12 |11796001 |11812968|TSS |strong_enhancer |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr12 |11796001 |11812968|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A11796001%2D11812968)|strong_enhancer |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ETV6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ETV6_protein_hg38.html)
33
+
34
+![image](../../images/proteinpaint/ETV6_NM_001987.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ETV6.html)
37
+
38
+![image](../../images/proteinpaint/ETV6.svg)
EXOSC6.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.46 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0 |0 |
22 21
|DLBCL |No |No |0 |0 |
23 22
|FL |No |No |0 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EXOSC6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EXOSC6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EXOSC6_NM_058219.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EXOSC6.html)
7
+
8
+![image](../../images/proteinpaint/EXOSC6.svg)
EZH2.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 3.46 |
16 15
|BL |Thomas cohort | 1.30 |
17 16
|BL |Panea cohort |10.90 |
18
-|DLBCL |GAMBL genomes |12.20 |
17
+|DLBCL |GAMBL genomes |13.77 |
19 18
|DLBCL |Schmitz cohort | 9.10 |
20 19
|DLBCL |Reddy cohort | 8.90 |
21 20
|DLBCL |Chapuy cohort | 5.60 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 4.992 |0 |
29 28
|DLBCL |No |Yes | 19.753 |0 |
30 29
|FL |No |Yes |117.987 |0 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2010 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/20081860). First described in FL in 2010 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/20081860)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2010 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/20081860). First described in FL in 2010 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/20081860)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZH2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZH2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/EZH2_NM_001203247.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZH2.html)
7
+
8
+![image](../../images/proteinpaint/EZH2.svg)
FAM129B.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.948 | 0.000 |
22 21
|DLBCL |No |No |0.000 |13.541 |
23 22
|FL |No |No |2.483 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM129B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM129B_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM129B.html)
5
+
6
+![image](../../images/proteinpaint/FAM129B.svg)
FAS.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 2.08 |
16 15
|BL |Thomas cohort | 1.70 |
17 16
|BL |Panea cohort | 4.00 |
18
-|DLBCL |GAMBL genomes | 8.80 |
17
+|DLBCL |GAMBL genomes | 9.18 |
19 18
|DLBCL |Schmitz cohort |10.90 |
20 19
|DLBCL |Reddy cohort | 4.70 |
21 20
|DLBCL |Chapuy cohort | 9.00 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 6.699 | 0.000 |
29 28
|DLBCL |No |Yes |16.878 |179.289 |
30 29
|FL |No |Yes | 0.000 |176.866 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAS_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAS_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/FAS_NM_000043.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAS.html)
38
+
39
+![image](../../images/proteinpaint/FAS.svg)
FBXO11.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|23.79 |
15 14
|BL |Thomas cohort |21.60 |
16 15
|BL |Panea cohort |15.80 |
17
-|DLBCL |GAMBL genomes | 4.10 |
16
+|DLBCL |GAMBL genomes | 3.82 |
18 17
|DLBCL |Schmitz cohort | 2.10 |
19 18
|DLBCL |Reddy cohort | 2.10 |
20 19
|DLBCL |Chapuy cohort | 2.60 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |14.801 |114.063 |
27 26
|DLBCL |No |Yes | 2.464 | 39.449 |
28 27
|FL |No |No | 8.837 | 0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743)
... ...
\ No newline at end of file
0
+> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXO11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXO11_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FBXO11_NM_025133.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXO11.html)
7
+
8
+![image](../../images/proteinpaint/FBXO11.svg)
FBXW7.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|3.0 |
15 14
|DLBCL |Reddy cohort |1.3 |
16 15
|DLBCL |Chapuy cohort |1.7 |
... ...
@@ -18,8 +17,17 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.846 | 0.000 |
23 22
|DLBCL |No |No |2.734 |10.734 |
24 23
|FL |No |No |2.987 |22.593 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXW7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXW7_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/FBXW7_NM_033632.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXW7.html)
32
+
33
+![image](../../images/proteinpaint/FBXW7.svg)
FGFR3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.974 |0 |
22 21
|DLBCL |No |No |1.140 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FGFR3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FGFR3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FGFR3_NM_000142.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FGFR3.html)
7
+
8
+![image](../../images/proteinpaint/FGFR3.svg)
FIP1L1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|5.31 |
14 13
|BL |Thomas cohort |2.50 |
15 14
|BL |Panea cohort |2.00 |
... ...
@@ -17,8 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |Yes |1.128 |47.630 |
22 21
|DLBCL |No |No |1.343 |10.476 |
23 22
|FL |No |No |3.166 | 0.000 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FIP1L1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FIP1L1_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/FIP1L1_NM_030917.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FIP1L1.html)
31
+
32
+![image](../../images/proteinpaint/FIP1L1.svg)
FLYWCH1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0 |13.882 |
22 21
|DLBCL |No |No |0 | 0.000 |
23 22
|FL |No |No |0 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FLYWCH1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FLYWCH1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FLYWCH1_NM_032296.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FLYWCH1.html)
7
+
8
+![image](../../images/proteinpaint/FLYWCH1.svg)
FOXC1.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|4.5 |
15
-|DLBCL |Reddy cohort |1.2 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|4.50 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |0.824 |0 |
24 23
|FL |No |No |1.906 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXC1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXC1_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/FOXC1_NM_001453.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXC1.html)
32
+
33
+![image](../../images/proteinpaint/FOXC1.svg)
FOXO1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|23.33 |
16 15
|BL |Thomas cohort |28.00 |
17 16
|BL |Panea cohort |21.80 |
18
-|DLBCL |GAMBL genomes |10.60 |
17
+|DLBCL |GAMBL genomes |10.13 |
19 18
|DLBCL |Schmitz cohort | 7.20 |
20 19
|DLBCL |Reddy cohort | 2.40 |
21 20
|DLBCL |Chapuy cohort | 2.10 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |14.841 | 5.170 |
29 28
|DLBCL |No |No | 6.936 | 0.000 |
30 29
|FL |No |Yes |18.992 |103.028 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXO1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXO1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FOXO1_NM_002015.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXO1.html)
7
+
8
+![image](../../images/proteinpaint/FOXO1.svg)
FOXP1.md
... ...
@@ -2,37 +2,45 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|1.9 |
15
-|DLBCL |Reddy cohort |2.1 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |1.218 | 9.469 |
23 22
|DLBCL |Yes |No |7.387 |17.777 |
24 23
|FL |Yes |No |0.000 | 0.000 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region |regulatory_comment|
29
-|--------|----------|--------|---------|------------------|
30
-|chr3 |71104986 |71119518|TSS-4 |active_promoter |
31
-|chr3 |71176427 |71180960|TSS-3 |active_promoter |
32
-|chr3 |71350633 |71357665|TSS-2 |active_promoter |
33
-|chr3 |71503103 |71504870|intron-1b|intron |
34
-|chr3 |71550753 |71551478|intron-1a|intron |
35
-|chr3 |71626341 |71635648|TSS-1 |active_promoter |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr3 |71104986 |71119518|[TSS-4](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A71104986%2D71119518) |active_promoter |
30
+|chr3 |71176427 |71180960|[TSS-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A71176427%2D71180960) |active_promoter |
31
+|chr3 |71350633 |71357665|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A71350633%2D71357665) |active_promoter |
32
+|chr3 |71503103 |71504870|[intron-1b](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A71503103%2D71504870)|intron |
33
+|chr3 |71550753 |71551478|[intron-1a](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A71550753%2D71551478)|intron |
34
+|chr3 |71626341 |71635648|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A71626341%2D71635648) |active_promoter |
36 35
37 36
> [!NOTE]
38
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FOXP1_NM_001349338.svg
5
+images/proteinpaint/FOXP1_NM_032682.svg)
6
+
7
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXP1.html)
8
+
9
+![image](../../images/proteinpaint/FOXP1.svg)
FTCD.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.23 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |3.359 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FTCD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FTCD_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FTCD_NM_206965.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FTCD.html)
7
+
8
+![image](../../images/proteinpaint/FTCD.svg)
FUBP1.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|1.5 |
15 14
|DLBCL |Reddy cohort |1.5 |
16 15
|DLBCL |Chapuy cohort |0.9 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.886 | 6.918 |
23 22
|DLBCL |No |No |0.000 | 9.093 |
24 23
|FL |No |No |7.430 |26.002 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FUBP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FUBP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FUBP1_NM_003902.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FUBP1.html)
7
+
8
+![image](../../images/proteinpaint/FUBP1.svg)
FUT5.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.2 |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort |0.3 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort |0.30 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |3.328 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FUT5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FUT5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FUT5_NM_002034.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FUT5.html)
7
+
8
+![image](../../images/proteinpaint/FUT5.svg)
FZD3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.23 |
14 13
|BL |Thomas cohort |0.00 |
15 14
|BL |Panea cohort |1.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |1.522 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FZD3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FZD3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/FZD3_NM_017412.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FZD3.html)
7
+
8
+![image](../../images/proteinpaint/FZD3.svg)
FZR1.md
... ...
@@ -0,0 +1,24 @@
1
+# [FZR1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|1.15 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No | 1.365 |0 |
19
+|DLBCL |No |No | 4.444 |0 |
20
+|FL |No |No |12.412 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
GABRA2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|2.6 |
15
-|DLBCL |Reddy cohort |1.2 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|2.60 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |8.135 |
23 22
|DLBCL |No |No |0.502 |0.000 |
24 23
|FL |No |No |1.493 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GABRA2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GABRA2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GABRA2_NM_000807.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GABRA2.html)
7
+
8
+![image](../../images/proteinpaint/GABRA2.svg)
GAK.md
... ...
@@ -0,0 +1,27 @@
1
+# [GAK]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |3.849 |0.000 |
22
+|DLBCL |No |No |0.798 |9.151 |
23
+|FL |No |No |0.000 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
GBP7.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.23 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.582 |0 |
20 19
|DLBCL |No |No |0.000 |0 |
21 20
|FL |No |No |0.000 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GBP7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GBP7_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GBP7_NM_207398.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GBP7.html)
7
+
8
+![image](../../images/proteinpaint/GBP7.svg)
GGTLA4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,8 +16,14 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GGTLA4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GGTLA4_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GGTLA4.html)
5
+
6
+![image](../../images/proteinpaint/GGTLA4.svg)
GNA13.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|21.02 |
16 15
|BL |Thomas cohort |21.60 |
17 16
|BL |Panea cohort |20.80 |
18
-|DLBCL |GAMBL genomes |11.70 |
17
+|DLBCL |GAMBL genomes |11.66 |
19 18
|DLBCL |Schmitz cohort | 8.50 |
20 19
|DLBCL |Reddy cohort |11.90 |
21 20
|DLBCL |Chapuy cohort |10.30 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |51.517 |966.741 |
29 28
|DLBCL |No |Yes |38.484 |284.077 |
30 29
|FL |No |Yes |48.688 |215.216 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNA13_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNA13_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GNA13_NM_006572.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNA13.html)
7
+
8
+![image](../../images/proteinpaint/GNA13.svg)
GNAI2.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|11.32 |
16 15
|BL |Thomas cohort | 9.70 |
17 16
|BL |Panea cohort | 8.90 |
18
-|DLBCL |GAMBL genomes | 4.70 |
17
+|DLBCL |GAMBL genomes | 5.35 |
19 18
|DLBCL |Schmitz cohort | 6.40 |
20 19
|DLBCL |Reddy cohort | 1.90 |
21 20
|DLBCL |Chapuy cohort | 3.80 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |18.304 | 0.000 |
29 28
|DLBCL |No |Yes |32.161 |57.623 |
30 29
|FL |No |Yes |55.205 | 0.000 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNAI2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNAI2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GNAI2_NM_002070.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNAI2.html)
7
+
8
+![image](../../images/proteinpaint/GNAI2.svg)
GNAS.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
14
-|DLBCL |Schmitz cohort|3.2 |
15
-|DLBCL |Reddy cohort |1.9 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.064 |13.8 |
23 22
|DLBCL |No |No |0.967 | 0.0 |
24 23
|FL |No |No |1.581 | 0.0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNAS_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNAS_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GNAS_NM_000516.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GNAS.html)
7
+
8
+![image](../../images/proteinpaint/GNAS.svg)
GOLGA5.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|0.9 |
15
-|DLBCL |Reddy cohort |1.9 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|0.90 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.362 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |3.693 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GOLGA5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GOLGA5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GOLGA5_NM_005113.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GOLGA5.html)
7
+
8
+![image](../../images/proteinpaint/GOLGA5.svg)
GPC5.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|1.9 |
15
-|DLBCL |Reddy cohort |2.2 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Reddy cohort |2.20 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.380 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |1.144 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GPC5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GPC5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GPC5_NM_004466.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GPC5.html)
7
+
8
+![image](../../images/proteinpaint/GPC5.svg)
GRB2.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|0.46 |
15 14
|BL |Thomas cohort |0.40 |
16 15
|BL |Panea cohort |1.00 |
17
-|DLBCL |GAMBL genomes |3.40 |
16
+|DLBCL |GAMBL genomes |3.25 |
18 17
|DLBCL |Schmitz cohort |2.80 |
19 18
|DLBCL |Reddy cohort |1.50 |
20 19
|DLBCL |Chapuy cohort |3.00 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No | 7.253 | 0.000 |
27 26
|DLBCL |No |Yes |33.029 |168.982 |
28 27
|FL |No |No | 8.575 | 0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRB2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GRB2_NM_002086.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRB2.html)
7
+
8
+![image](../../images/proteinpaint/GRB2.svg)
GRHPR.md
... ...
@@ -2,29 +2,37 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|4.5 |
15
-|DLBCL |Reddy cohort |3.6 |
16
-|DLBCL |Chapuy cohort |4.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|4.50 |
14
+|DLBCL |Reddy cohort |3.60 |
15
+|DLBCL |Chapuy cohort |4.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No | 1.819 | 0.000 |
23 22
|DLBCL |Yes |Yes |10.245 |60.346 |
24 23
|FL |Yes |No | 0.000 | 0.000 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr9 |37423010 |37425279|TSS |active_promoter |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29
+|chr9 |37423010 |37425279|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37423010%2D37425279)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRHPR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRHPR_protein_hg38.html)
33
+
34
+![image](../../images/proteinpaint/GRHPR_NM_012203.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRHPR.html)
37
+
38
+![image](../../images/proteinpaint/GRHPR.svg)
GRIK5.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.92 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.060 |0 |
22 21
|DLBCL |No |No |2.412 |0 |
23 22
|FL |No |No |1.801 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIK5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIK5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GRIK5_NM_002088.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIK5.html)
7
+
8
+![image](../../images/proteinpaint/GRIK5.svg)
GRM6.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.92 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.95 |0 |
20 19
|DLBCL |No |No |1.43 |0 |
21 20
|FL |No |No |0.00 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRM6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRM6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GRM6_NM_000843.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRM6.html)
7
+
8
+![image](../../images/proteinpaint/GRM6.svg)
GSG2.md
... ...
@@ -2,27 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|4.0 |
15
-|DLBCL |Reddy cohort |1.5 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|4.00 |
14
+|DLBCL |Reddy cohort |1.50 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.723 |0 |
23 22
|DLBCL |No |No |3.101 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GSG2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GSG2_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GSG2.html)
5
+
6
+![image](../../images/proteinpaint/GSG2.svg)
GTSE1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.224 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GTSE1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GTSE1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/GTSE1_NM_016426.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GTSE1.html)
7
+
8
+![image](../../images/proteinpaint/GTSE1.svg)
HIST1H1B.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|4.62 |
16 15
|BL |Thomas cohort |5.50 |
17 16
|BL |Panea cohort |4.00 |
18
-|DLBCL |GAMBL genomes |9.30 |
17
+|DLBCL |GAMBL genomes |8.41 |
19 18
|DLBCL |Schmitz cohort |8.50 |
20 19
|DLBCL |Reddy cohort |7.30 |
21 20
|DLBCL |Chapuy cohort |9.80 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes | 6.345 |34.135 |
29 28
|DLBCL |No |Yes | 5.595 | 0.000 |
30 29
|FL |No |No |19.175 | 0.000 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1B_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/HIST1H1B_NM_005322.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1B.html)
38
+
39
+![image](../../images/proteinpaint/HIST1H1B.svg)
HIST1H1C.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 4.85 |
16 15
|BL |Thomas cohort | 3.80 |
17 16
|BL |Panea cohort | 9.90 |
18
-|DLBCL |GAMBL genomes |11.70 |
17
+|DLBCL |GAMBL genomes | 9.94 |
19 18
|DLBCL |Schmitz cohort | 9.80 |
20 19
|DLBCL |Reddy cohort | 9.40 |
21 20
|DLBCL |Chapuy cohort |12.40 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |10.205 |0 |
29 28
|DLBCL |No |Yes | 9.354 |0 |
30 29
|FL |No |No | 4.446 |0 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1C_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H1C_NM_005319.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1C.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H1C.svg)
HIST1H1D.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|3.23 |
16 15
|BL |Thomas cohort |4.70 |
17 16
|BL |Panea cohort |4.00 |
18
-|DLBCL |GAMBL genomes |6.50 |
17
+|DLBCL |GAMBL genomes |6.12 |
19 18
|DLBCL |Schmitz cohort |5.70 |
20 19
|DLBCL |Reddy cohort |6.10 |
21 20
|DLBCL |Chapuy cohort |7.70 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |8.064 |0 |
29 28
|DLBCL |No |No |2.458 |0 |
30 29
|FL |No |No |0.857 |0 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1D_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/HIST1H1D_NM_005320.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1D.html)
38
+
39
+![image](../../images/proteinpaint/HIST1H1D.svg)
HIST1H1E.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 9.70 |
16 15
|BL |Thomas cohort | 7.60 |
17 16
|BL |Panea cohort |19.80 |
18
-|DLBCL |GAMBL genomes |16.50 |
17
+|DLBCL |GAMBL genomes |18.55 |
19 18
|DLBCL |Schmitz cohort |17.90 |
20 19
|DLBCL |Reddy cohort |14.50 |
21 20
|DLBCL |Chapuy cohort |11.50 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |14.203 |0.000 |
29 28
|DLBCL |No |Yes | 4.446 |6.437 |
30 29
|FL |No |Yes |10.043 |0.000 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1E_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1E_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H1E_NM_005321.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1E.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H1E.svg)
HIST1H2AC.md
... ...
@@ -2,26 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |5.90 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |5.16 |
15 14
|DLBCL |Schmitz cohort|6.20 |
16 15
|DLBCL |Reddy cohort |3.40 |
17 16
|DLBCL |Chapuy cohort |6.40 |
18
-|FL |GAMBL genomes |2.08 |
17
+|FL |GAMBL genomes |2.31 |
19 18
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |1.742 | 0.000 |
25 24
|DLBCL |No |No |3.090 |20.364 |
26 25
|FL |No |No |1.715 | 0.000 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AC_protein_hg38.html)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AC.html)
32
+
33
+![image](../../images/proteinpaint/HIST1H2AC.svg)
HIST1H2AG.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|1.39 |
15 14
|BL |Thomas cohort |2.50 |
16 15
|BL |Panea cohort |1.00 |
... ...
@@ -19,11 +18,19 @@
19 18
## Mutation pattern
20 19
21 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22
-|------|----|---------------------|----------------|----------------|
21
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23 22
|BL |No |No |3.809 |0 |
24 23
|DLBCL |No |No |5.602 |0 |
25 24
|FL |No |No |0.405 |0 |
26 25
27 26
28 27
> [!NOTE]
29
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AG_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AG_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H2AG_NM_021064.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AG.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H2AG.svg)
HIST1H2AM.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|1.85 |
16 15
|BL |Thomas cohort |1.70 |
17 16
|BL |Panea cohort |3.00 |
18
-|DLBCL |GAMBL genomes |6.10 |
17
+|DLBCL |GAMBL genomes |5.93 |
19 18
|DLBCL |Schmitz cohort |5.70 |
20 19
|DLBCL |Reddy cohort |4.80 |
21 20
|DLBCL |Chapuy cohort |6.00 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |2.149 |0 |
29 28
|DLBCL |No |No |1.844 |0 |
30 29
|FL |No |No |1.845 |0 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AM_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AM_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H2AM_NM_003514.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2AM.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H2AM.svg)
HIST1H2BC.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |4.10 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |4.59 |
15 14
|DLBCL |Schmitz cohort|5.50 |
16 15
|DLBCL |Reddy cohort |4.30 |
17 16
|DLBCL |Chapuy cohort |5.60 |
... ...
@@ -20,11 +19,17 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |2.806 |35.161 |
25 24
|DLBCL |No |No |1.712 | 0.000 |
26 25
|FL |No |No |1.094 | 0.000 |
27 26
28 27
29 28
> [!NOTE]
30
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BC_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BC.html)
5
+
6
+![image](../../images/proteinpaint/HIST1H2BC.svg)
HIST1H2BD.md
... ...
@@ -2,21 +2,27 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.15 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.524 |0 |
20 19
|DLBCL |No |No |0.671 |0 |
21 20
|FL |No |No |1.751 |0 |
22 21
22
+
23
+
24
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD_protein_hg38.html)
25
+
26
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD.html)
27
+
28
+![image](../../images/proteinpaint/HIST1H2BD.svg)
HIST1H2BG.md
... ...
@@ -2,21 +2,27 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|2.08 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.350 |0 |
20 19
|DLBCL |No |No |3.197 |0 |
21 20
|FL |No |No |1.211 |0 |
22 21
22
+
23
+
24
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG_protein_hg38.html)
25
+
26
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG.html)
27
+
28
+![image](../../images/proteinpaint/HIST1H2BG.svg)
HIST1H2BK.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|5.31 |
15 14
|BL |Thomas cohort |4.70 |
16 15
|BL |Panea cohort |7.90 |
17
-|DLBCL |GAMBL genomes |5.40 |
16
+|DLBCL |GAMBL genomes |4.59 |
18 17
|DLBCL |Schmitz cohort |4.90 |
19 18
|DLBCL |Reddy cohort |4.20 |
20 19
|DLBCL |Chapuy cohort |5.60 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |4.421 |0 |
27 26
|DLBCL |No |No |1.567 |0 |
28 27
|FL |No |No |0.760 |0 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BK_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H2BK_NM_080593.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BK.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H2BK.svg)
HIST1H2BM.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.69 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |2.367 |54.179 |
20 19
|DLBCL |No |No |1.312 | 0.000 |
21 20
|FL |No |No |1.980 | 0.000 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BM_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BM_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H2BM_NM_003521.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BM.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H2BM.svg)
HIST1H3B.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |2.00 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |2.10 |
15 14
|DLBCL |Schmitz cohort|1.70 |
16 15
|DLBCL |Reddy cohort |2.00 |
17 16
|DLBCL |Chapuy cohort |2.10 |
... ...
@@ -20,8 +19,15 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |8.244 |0.000 |
25 24
|DLBCL |No |No |2.108 |9.678 |
26 25
|FL |No |No |1.637 |0.000 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3B_protein_hg38.html)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3B.html)
32
+
33
+![image](../../images/proteinpaint/HIST1H3B.svg)
HIST1H3D.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.31 |
14 13
|BL |Thomas cohort |1.70 |
15 14
|BL |Panea cohort |3.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.566 |0 |
22 21
|DLBCL |No |No |2.153 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3D_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H3D_NM_003530.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3D.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H3D.svg)
HIST1H3G.md
... ...
@@ -2,21 +2,29 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.62 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.701 |0.000 |
20 19
|DLBCL |No |No |0.517 |5.984 |
21 20
|FL |No |No |3.230 |0.000 |
22 21
22
+
23
+
24
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3G_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3G_protein_hg38.html)
25
+
26
+![image](../../images/proteinpaint/HIST1H3G_NM_003534.svg)
27
+
28
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3G.html)
29
+
30
+![image](../../images/proteinpaint/HIST1H3G.svg)
HIST1H3H.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort |1.30 |
15 14
|BL |Panea cohort |5.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.791 |0 |
22 21
|DLBCL |No |No |1.257 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3H_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3H_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H3H_NM_003536.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3H.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H3H.svg)
HIST1H3I.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|FL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|FL |2 |relevance in FL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|0.46 |
15 14
|BL |Thomas cohort |0.00 |
16 15
|BL |Panea cohort |2.00 |
... ...
@@ -19,11 +18,19 @@
19 18
## Mutation pattern
20 19
21 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22
-|------|----|---------------------|----------------|----------------|
21
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23 22
|BL |No |No |0.000 |0 |
24 23
|DLBCL |No |No |5.397 |0 |
25 24
|FL |No |No |0.838 |0 |
26 25
27 26
28 27
> [!NOTE]
29
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3I_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3I_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H3I_NM_003533.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3I.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H3I.svg)
HIST1H3J.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.31 |
14 13
|BL |Thomas cohort |1.70 |
15 14
|BL |Panea cohort |5.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |6.396 |0 |
22 21
|DLBCL |No |No |1.417 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3J_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3J_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H3J_NM_003535.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3J.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H3J.svg)
HIST1H4J.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.46 |
14 13
|BL |Thomas cohort |0.40 |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.955 |0 |
22 21
|DLBCL |No |No |1.504 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H4J_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H4J_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HIST1H4J_NM_021968.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H4J.html)
7
+
8
+![image](../../images/proteinpaint/HIST1H4J.svg)
HIST2H2BE.md
... ...
@@ -2,24 +2,30 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|3.2 |
15
-|DLBCL |Reddy cohort |2.6 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Reddy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.780 |40.980 |
23 22
|DLBCL |No |No |0.601 | 3.291 |
24 23
|FL |No |No |3.156 | 0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE_protein_hg38.html)
28
+
29
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE.html)
30
+
31
+![image](../../images/proteinpaint/HIST2H2BE.svg)
HLA-A.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 1.39 |
15 14
|BL |Thomas cohort | 1.30 |
16 15
|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes | 8.80 |
16
+|DLBCL |GAMBL genomes | 7.46 |
18 17
|DLBCL |Schmitz cohort |11.10 |
19 18
|DLBCL |Reddy cohort | 0.20 |
20 19
|DLBCL |Chapuy cohort | 9.00 |
... ...
@@ -22,8 +21,16 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No | 4.995 | 22.371 |
27 26
|DLBCL |No |Yes |14.841 |190.534 |
28 27
|FL |No |No | 0.000 | 0.000 |
29 28
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-A_protein_hg38.html)
31
+
32
+![image](../../images/proteinpaint/HLA-A_NM_002116.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-A.html)
35
+
36
+![image](../../images/proteinpaint/HLA-A.svg)
HLA-B.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 3.46 |
16 15
|BL |Thomas cohort | 3.80 |
17 16
|BL |Panea cohort | 5.00 |
18
-|DLBCL |GAMBL genomes | 9.50 |
17
+|DLBCL |GAMBL genomes | 9.18 |
19 18
|DLBCL |Schmitz cohort |16.40 |
20 19
|DLBCL |Reddy cohort | 1.20 |
21 20
|DLBCL |Chapuy cohort |10.70 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes | 6.598 | 94.947 |
29 28
|DLBCL |No |Yes |27.361 |222.398 |
30 29
|FL |No |No | 0.000 | 88.288 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-B_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/HLA-B_NM_005514.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-B.html)
38
+
39
+![image](../../images/proteinpaint/HLA-B.svg)
HLA-C.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.1 |
14
-|DLBCL |Schmitz cohort|5.5 |
15
-|DLBCL |Reddy cohort | NA |
16
-|DLBCL |Chapuy cohort |4.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.63 |
13
+|DLBCL |Schmitz cohort|5.50 |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort |4.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.687 | 0.000 |
23 22
|DLBCL |No |Yes |6.500 |33.396 |
24 23
|FL |No |No |0.000 | 0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-C_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/HLA-C_NM_002117.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-C.html)
32
+
33
+![image](../../images/proteinpaint/HLA-C.svg)
HLA-DMA.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort | NA |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.255 | 0.000 |
23 22
|DLBCL |No |No |3.359 |38.853 |
24 23
|FL |No |No |0.000 |76.864 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMA_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/HLA-DMA_NM_006120.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMA.html)
32
+
33
+![image](../../images/proteinpaint/HLA-DMA.svg)
HLA-DMB.md
... ...
@@ -2,28 +2,36 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
14
-|BL |GAMBL genomes+capture| NA |
15
-|BL |Thomas cohort |0.0 |
16
-|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |3.4 |
18
-|DLBCL |Schmitz cohort |5.1 |
19
-|DLBCL |Reddy cohort | NA |
20
-|DLBCL |Chapuy cohort |1.7 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture| NA |
14
+|BL |Thomas cohort |0.00 |
15
+|BL |Panea cohort | NA |
16
+|DLBCL |GAMBL genomes |3.82 |
17
+|DLBCL |Schmitz cohort |5.10 |
18
+|DLBCL |Reddy cohort | NA |
19
+|DLBCL |Chapuy cohort |1.70 |
21 20
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No | 0.000 | 0.000 |
27 26
|DLBCL |No |Yes |16.721 | 26.750 |
28 27
|FL |No |Yes |39.781 |282.532 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMB_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/HLA-DMB_NM_002118.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMB.html)
36
+
37
+![image](../../images/proteinpaint/HLA-DMB.svg)
HLA-DQA1.md
... ...
@@ -0,0 +1,27 @@
1
+# [HLA-DQA1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0 |0 |
22
+|DLBCL |No |No |0 |0 |
23
+|FL |No |No |0 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
HLA-DQB1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0 |0 |
22 21
|DLBCL |No |No |0 |0 |
23 22
|FL |No |No |0 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DQB1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DQB1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HLA-DQB1_NM_002123.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DQB1.html)
7
+
8
+![image](../../images/proteinpaint/HLA-DQB1.svg)
HNF1B.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.2 |
14
-|DLBCL |Schmitz cohort|2.6 |
15
-|DLBCL |Reddy cohort |0.3 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|2.60 |
14
+|DLBCL |Reddy cohort |0.30 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |2.652 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNF1B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNF1B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HNF1B_NM_000458.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNF1B.html)
7
+
8
+![image](../../images/proteinpaint/HNF1B.svg)
HNRNPD.md
... ...
@@ -2,26 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene |
8
+|FL |2 |relevance in FL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |2.7 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |2.1 |
15 14
|DLBCL |Schmitz cohort|2.1 |
16 15
|DLBCL |Reddy cohort |1.8 |
17 16
|DLBCL |Chapuy cohort |0.9 |
18
-|FL |GAMBL genomes |0.0 |
17
+|FL |GAMBL genomes | NA |
19 18
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |0.000 |19.81 |
25 24
|DLBCL |No |No |1.554 | 0.00 |
26 25
|FL |No |No |0.000 | 0.00 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPD_protein_hg38.html)
30
+
31
+![image](../../images/proteinpaint/HNRNPD_NM_031370.svg)
32
+
33
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPD.html)
34
+
35
+![image](../../images/proteinpaint/HNRNPD.svg)
HNRNPH1.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|3.2 |
15 14
|DLBCL |Reddy cohort |1.4 |
16 15
|DLBCL |Chapuy cohort |3.4 |
... ...
@@ -18,8 +17,17 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.573 | 0.000 |
23 22
|DLBCL |No |No |2.337 |10.139 |
24 23
|FL |No |No |0.000 | 0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPH1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPH1_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/HNRNPH1_NM_005520.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPH1.html)
32
+
33
+![image](../../images/proteinpaint/HNRNPH1.svg)
HNRNPU.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|5.77 |
15 14
|BL |Thomas cohort |6.40 |
16 15
|BL |Panea cohort |8.90 |
17
-|DLBCL |GAMBL genomes |1.80 |
16
+|DLBCL |GAMBL genomes |2.49 |
18 17
|DLBCL |Schmitz cohort |3.40 |
19 18
|DLBCL |Reddy cohort |2.40 |
20 19
|DLBCL |Chapuy cohort |3.40 |
... ...
@@ -22,16 +21,24 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |Yes |1.081 |27.052 |
27 26
|DLBCL |Yes |No |1.712 | 0.000 |
28 27
|FL |Yes |No |4.865 |31.056 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
33
-|--------|----------|---------|------|------------------|
34
-|chr1 |245023502 |245029083|TSS |NA |
31
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
32
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr1 |245023502 |245029083|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A245023502%2D245029083)|NA |
35 34
36 35
> [!NOTE]
37
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HNRNPU_NM_031844.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU.html)
7
+
8
+![image](../../images/proteinpaint/HNRNPU.svg)
HRAS.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes | NA |
14 13
|DLBCL |Schmitz cohort|0.2 |
15 14
|DLBCL |Reddy cohort |0.7 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 |0 |
23 22
|DLBCL |No |No |0 |0 |
24 23
|FL |No |No |0 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HRAS_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HRAS_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/HRAS_NM_005343.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HRAS.html)
7
+
8
+![image](../../images/proteinpaint/HRAS.svg)
HVCN1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|0.92 |
16 15
|BL |Thomas cohort |0.80 |
17 16
|BL |Panea cohort |2.00 |
18
-|DLBCL |GAMBL genomes |3.20 |
17
+|DLBCL |GAMBL genomes |3.06 |
19 18
|DLBCL |Schmitz cohort |1.90 |
20 19
|DLBCL |Reddy cohort |2.30 |
21 20
|DLBCL |Chapuy cohort |3.40 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 2.588 | 0.000 |
29 28
|DLBCL |No |Yes | 7.172 | 47.127 |
30 29
|FL |No |Yes |16.103 |259.368 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HVCN1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HVCN1_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/HVCN1_NM_001040107.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HVCN1.html)
38
+
39
+![image](../../images/proteinpaint/HVCN1.svg)
ICK.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.69 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.813 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ICK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ICK_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ICK.html)
5
+
6
+![image](../../images/proteinpaint/ICK.svg)
ID3.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |2 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|FL |2 |relevance in FL not firmly established |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|45.50 |
16 15
|BL |Thomas cohort |47.00 |
17 16
|BL |Panea cohort |31.70 |
18
-|DLBCL |GAMBL genomes | 2.00 |
17
+|DLBCL |GAMBL genomes | 1.53 |
19 18
|DLBCL |Schmitz cohort | 4.70 |
20 19
|DLBCL |Reddy cohort | 3.50 |
21 20
|DLBCL |Chapuy cohort | 0.90 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |Yes |42.419 |439.808 |
29 28
|DLBCL |Yes |Yes | 0.000 | 30.520 |
30 29
|FL |Yes |No | 3.497 | 0.000 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr1 |23885584 |23885835|TSS |NA |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
35
+|chr1 |23885584 |23885835|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A23885584%2D23885835)|NA |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2012 by [Richter J](https://pubmed.ncbi.nlm.nih.gov/23143595). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Richter J](https://pubmed.ncbi.nlm.nih.gov/23143595). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ID3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ID3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ID3_NM_002167.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ID3.html)
7
+
8
+![image](../../images/proteinpaint/ID3.svg)
IGLL5.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|FL |2 |relevance in FL not firmly established |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|26.33 |
16 15
|BL |Thomas cohort |25.00 |
17 16
|BL |Panea cohort |23.80 |
18
-|DLBCL |GAMBL genomes |41.10 |
17
+|DLBCL |GAMBL genomes |41.49 |
19 18
|DLBCL |Schmitz cohort |36.00 |
20 19
|DLBCL |Reddy cohort |16.10 |
21 20
|DLBCL |Chapuy cohort | 9.00 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |Yes |7.850 |3.210 |
29 28
|DLBCL |Yes |Yes |3.376 |5.315 |
30 29
|FL |Yes |Yes |4.830 |9.846 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr22 |23229554 |23232042|TSS |NA |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr22 |23229554 |23232042|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr22%3A23229554%2D23232042)|NA |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IGLL5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IGLL5_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/IGLL5_NM_001178126.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IGLL5.html)
43
+
44
+![image](../../images/proteinpaint/IGLL5.svg)
IKBKB.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|3.0 |
15
-|DLBCL |Reddy cohort |1.1 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|3.00 |
14
+|DLBCL |Reddy cohort |1.10 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |4.726 |0 |
23 22
|DLBCL |No |No |1.593 |0 |
24 23
|FL |No |No |3.189 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKBKB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKBKB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/IKBKB_NM_001556.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKBKB.html)
7
+
8
+![image](../../images/proteinpaint/IKBKB.svg)
IKBKE.md
... ...
@@ -0,0 +1,27 @@
1
+# [IKBKE]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.76 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.102 |0 |
22
+|DLBCL |No |No |3.279 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
IKZF3.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|1.62 |
15 14
|BL |Thomas cohort |0.80 |
16 15
|BL |Panea cohort |3.00 |
17
-|DLBCL |GAMBL genomes |4.30 |
16
+|DLBCL |GAMBL genomes |4.78 |
18 17
|DLBCL |Schmitz cohort |4.50 |
19 18
|DLBCL |Reddy cohort |3.90 |
20 19
|DLBCL |Chapuy cohort |4.30 |
... ...
@@ -22,17 +21,25 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |No | 1.552 |0 |
27 26
|DLBCL |Yes |No |10.924 |0 |
28 27
|FL |Yes |No | 7.180 |0 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
33
-|--------|----------|--------|------|------------------|
34
-|chr17 |37928959 |37940119|TSS-1 |NA |
35
-|chr17 |38015776 |38024832|TSS-2 |NA |
31
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
32
+|:--------:|:----------:|:--------:|:--------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr17 |37928959 |37940119|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A37928959%2D37940119)|NA |
34
+|chr17 |38015776 |38024832|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A38015776%2D38024832)|NA |
36 35
37 36
> [!NOTE]
38
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2017 by [Mareschal S](https://pubmed.ncbi.nlm.nih.gov/28479318)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2017 by [Mareschal S](https://pubmed.ncbi.nlm.nih.gov/28479318)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKZF3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKZF3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/IKZF3_NM_012481.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKZF3.html)
7
+
8
+![image](../../images/proteinpaint/IKZF3.svg)
IL16.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.3 |
14
-|DLBCL |Schmitz cohort|3.8 |
15
-|DLBCL |Reddy cohort |2.8 |
16
-|DLBCL |Chapuy cohort |5.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|3.80 |
14
+|DLBCL |Reddy cohort |2.80 |
15
+|DLBCL |Chapuy cohort |5.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.941 |0 |
23 22
|DLBCL |No |No |1.966 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL16_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL16_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/IL16_NM_004513.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL16.html)
32
+
33
+![image](../../images/proteinpaint/IL16.svg)
IL4R.md
... ...
@@ -2,32 +2,39 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|2.1 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |3.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|2.10 |
14
+|DLBCL |Reddy cohort |2.50 |
15
+|DLBCL |Chapuy cohort |3.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |3.355 |0 |
23 22
|DLBCL |Yes |No |9.640 |0 |
24 23
|FL |Yes |No |0.000 |0 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr16 |27322895 |27329423|TSS |active_promoter |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr16 |27322895 |27329423|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A27322895%2D27329423)|active_promoter |
31 30
32 31
> [!NOTE]
33
-> First described in DLBCL in 2021 by [Duns G](https://pubmed.ncbi.nlm.nih.gov/33684939)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2021 by [Duns G](https://pubmed.ncbi.nlm.nih.gov/33684939)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL4R_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL4R_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/IL4R_NM_000418.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL4R.html)
7
+
8
+![image](../../images/proteinpaint/IL4R.svg)
IL6.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|2.8 |
15
-|DLBCL |Reddy cohort |1.2 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |4.532 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/IL6_NM_000600.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL6.html)
7
+
8
+![image](../../images/proteinpaint/IL6.svg)
INO80.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.4 |
14
-|DLBCL |Schmitz cohort|4.3 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|4.30 |
14
+|DLBCL |Reddy cohort |2.50 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.227 |0.000 |
23 22
|DLBCL |No |No |2.156 |5.706 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/INO80_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/INO80_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/INO80_NM_017553.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/INO80.html)
7
+
8
+![image](../../images/proteinpaint/INO80.svg)
IRF1.md
... ...
@@ -0,0 +1,32 @@
1
+# [IRF1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |2.409 | 0.000 |
22
+|DLBCL |Yes |No |2.468 |39.294 |
23
+|FL |Yes |No |6.465 | 0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr5 |131823933 |131826458|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A131823933%2D131826458)|active_promoter |
30
+
31
+> [!NOTE]
32
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
IRF4.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |3.20 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |4.40 |
15 14
|DLBCL |Schmitz cohort|7.00 |
16 15
|DLBCL |Reddy cohort |4.40 |
17 16
|DLBCL |Chapuy cohort |2.10 |
... ...
@@ -20,16 +19,24 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No | 0.000 |0 |
25 24
|DLBCL |Yes |Yes |25.817 |0 |
26 25
|FL |Yes |No | 0.000 |0 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
31
-|--------|----------|--------|------|------------------|
32
-|chr6 |390572 |394093 |TSS |active_promoter |
29
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
30
+|:--------:|:----------:|:--------:|:-------------------------------------------------------------------------------------:|:------------------:|
31
+|chr6 |390572 |394093 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A390572%2D394093)|active_promoter |
33 32
34 33
> [!NOTE]
35
-> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/IRF4_NM_002460.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF4.html)
7
+
8
+![image](../../images/proteinpaint/IRF4.svg)
IRF8.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 2.31 |
16 15
|BL |Thomas cohort | 1.30 |
17 16
|BL |Panea cohort | 6.90 |
18
-|DLBCL |GAMBL genomes | 8.80 |
17
+|DLBCL |GAMBL genomes | 8.03 |
19 18
|DLBCL |Schmitz cohort |10.40 |
20 19
|DLBCL |Reddy cohort | 7.60 |
21 20
|DLBCL |Chapuy cohort |10.30 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 1.360 | 0.000 |
29 28
|DLBCL |Yes |Yes | 6.806 | 0.000 |
30 29
|FL |Yes |Yes |28.663 |102.572 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr16 |85931918 |85933977|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr16 |85931918 |85933977|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A85931918%2D85933977)|active_promoter |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF8_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/IRF8_NM_002163.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF8.html)
43
+
44
+![image](../../images/proteinpaint/IRF8.svg)
ITPKB.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |6.50 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |6.69 |
15 14
|DLBCL |Schmitz cohort|6.80 |
16 15
|DLBCL |Reddy cohort |6.70 |
17 16
|DLBCL |Chapuy cohort |9.40 |
... ...
@@ -20,18 +19,26 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No |0.587 | 0.000 |
25 24
|DLBCL |Yes |Yes |4.294 |15.744 |
26 25
|FL |Yes |No |6.541 | 0.000 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end |region |regulatory_comment|
31
-|--------|----------|---------|--------|------------------|
32
-|chr1 |226864857 |226873452|intron |weak_enhancer |
33
-|chr1 |226920563 |226927885|TSS |active_promoter |
34
-|chr1 |226921088 |226927982|intron-1|enhancer |
29
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
30
+|:--------:|:----------:|:---------:|:------------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr1 |226864857 |226873452|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A226864857%2D226873452) |weak_enhancer |
32
+|chr1 |226920563 |226927885|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A226920563%2D226927885) |active_promoter |
33
+|chr1 |226921088 |226927982|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A226921088%2D226927982)|enhancer |
35 34
36 35
> [!NOTE]
37
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ITPKB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ITPKB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ITPKB_NM_002221.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ITPKB.html)
7
+
8
+![image](../../images/proteinpaint/ITPKB.svg)
ITPR3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.546 |0 |
22 21
|DLBCL |No |No |1.349 |0 |
23 22
|FL |No |No |1.332 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ITPR3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ITPR3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ITPR3_NM_002224.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ITPR3.html)
7
+
8
+![image](../../images/proteinpaint/ITPR3.svg)
JAK1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|1.9 |
15
-|DLBCL |Reddy cohort |2.2 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Reddy cohort |2.20 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.067 |0 |
23 22
|DLBCL |No |No |4.294 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JAK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JAK1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/JAK1_NM_002227.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JAK1.html)
7
+
8
+![image](../../images/proteinpaint/JAK1.svg)
JAK3.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.4 |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort |1.0 |
16
-|DLBCL |Chapuy cohort | NA |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort |1.00 |
15
+|DLBCL |Chapuy cohort | NA |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.034 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JAK3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JAK3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/JAK3_NM_000215.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JAK3.html)
7
+
8
+![image](../../images/proteinpaint/JAK3.svg)
JUNB.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|3.2 |
15
-|DLBCL |Reddy cohort |3.5 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.25 |
13
+|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Reddy cohort |3.50 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.009 |0.00 |
23 22
|DLBCL |No |No |1.285 |8.88 |
24 23
|FL |No |No |0.000 |0.00 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JUNB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JUNB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/JUNB_NM_002229.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JUNB.html)
7
+
8
+![image](../../images/proteinpaint/JUNB.svg)
JUP.md
... ...
@@ -0,0 +1,24 @@
1
+# [JUP]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|1.15 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.441 |8.462 |
19
+|DLBCL |No |No |4.770 |0.000 |
20
+|FL |No |No |8.023 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
KCMF1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|1.5 |
15
-|DLBCL |Reddy cohort |1.0 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|1.50 |
14
+|DLBCL |Reddy cohort |1.00 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |6.003 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KCMF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KCMF1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KCMF1_NM_020122.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KCMF1.html)
7
+
8
+![image](../../images/proteinpaint/KCMF1.svg)
KCNK10.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.92 |
14 13
|BL |Thomas cohort |0.80 |
15 14
|BL |Panea cohort |1.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.406 |0 |
22 21
|DLBCL |No |No |0.632 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KCNK10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KCNK10_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KCNK10_NM_021161.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KCNK10.html)
7
+
8
+![image](../../images/proteinpaint/KCNK10.svg)
KIFC3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.012 |5.98 |
22 21
|DLBCL |No |No |0.000 |0.00 |
23 22
|FL |No |No |2.064 |0.00 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIFC3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIFC3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KIFC3_NM_005550.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIFC3.html)
7
+
8
+![image](../../images/proteinpaint/KIFC3.svg)
KIR3DL1.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.15 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0 | 0.000 |
20 19
|DLBCL |No |No |0 |25.433 |
21 20
|FL |No |No |0 | 0.000 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIR3DL1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIR3DL1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KIR3DL1_NM_013289.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIR3DL1.html)
7
+
8
+![image](../../images/proteinpaint/KIR3DL1.svg)
KLF2.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |7.70 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |8.60 |
15 14
|DLBCL |Schmitz cohort|7.00 |
16 15
|DLBCL |Reddy cohort |2.10 |
17 16
|DLBCL |Chapuy cohort |3.00 |
... ...
@@ -20,16 +19,24 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No |2.274 |0 |
25 24
|DLBCL |Yes |No |3.067 |0 |
26 25
|FL |Yes |No |9.318 |0 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
31
-|--------|----------|--------|------|------------------|
32
-|chr19 |16434978 |16439011|TSS |intron |
29
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
30
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr19 |16434978 |16439011|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A16434978%2D16439011)|intron |
33 32
34 33
> [!NOTE]
35
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLF2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLF2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KLF2_NM_016270.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLF2.html)
7
+
8
+![image](../../images/proteinpaint/KLF2.svg)
KLHL14.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |5.0 |
14
-|DLBCL |Schmitz cohort|6.6 |
15
-|DLBCL |Reddy cohort |4.6 |
16
-|DLBCL |Chapuy cohort |7.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.59 |
13
+|DLBCL |Schmitz cohort|6.60 |
14
+|DLBCL |Reddy cohort |4.60 |
15
+|DLBCL |Chapuy cohort |7.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No | 0.000 | 0.000 |
23 22
|DLBCL |No |No | 3.154 | 2.846 |
24 23
|FL |No |No |12.248 |24.944 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL14_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL14_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KLHL14_NM_020805.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL14.html)
7
+
8
+![image](../../images/proteinpaint/KLHL14.svg)
KLHL21.md
... ...
@@ -2,32 +2,39 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.3 |
14
-|DLBCL |Schmitz cohort|4.7 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|4.70 |
14
+|DLBCL |Reddy cohort |2.50 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |0.000 |0 |
23 22
|DLBCL |Yes |No |1.741 |0 |
24 23
|FL |Yes |No |0.000 |0 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr1 |6661482 |6662702 |TSS |NA |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:---------------------------------------------------------------------------------------:|:------------------:|
29
+|chr1 |6661482 |6662702 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A6661482%2D6662702)|NA |
31 30
32 31
> [!NOTE]
33
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL21_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL21_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KLHL21_NM_014851.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL21.html)
7
+
8
+![image](../../images/proteinpaint/KLHL21.svg)
KLHL26.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.46 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.487 |0 |
22 21
|DLBCL |No |No |2.471 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL26_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL26_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KLHL26_NM_018316.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL26.html)
7
+
8
+![image](../../images/proteinpaint/KLHL26.svg)
KLHL6.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|3.93 |
16 15
|BL |Thomas cohort |3.00 |
17 16
|BL |Panea cohort |6.90 |
18
-|DLBCL |GAMBL genomes |5.20 |
17
+|DLBCL |GAMBL genomes |5.35 |
19 18
|DLBCL |Schmitz cohort |9.10 |
20 19
|DLBCL |Reddy cohort |6.40 |
21 20
|DLBCL |Chapuy cohort |9.00 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 4.630 | 0.000 |
29 28
|DLBCL |Yes |No | 7.379 | 6.684 |
30 29
|FL |Yes |Yes |20.169 |55.914 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment |
35
-|--------|----------|---------|------|-------------------------------|
36
-|chr3 |183269360 |183274139|TSS |active_promoter-strong_enhancer|
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment |
34
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:-------------------------------:|
35
+|chr3 |183269360 |183274139|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A183269360%2D183274139)|active_promoter-strong_enhancer|
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL6_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/KLHL6_NM_130446.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL6.html)
43
+
44
+![image](../../images/proteinpaint/KLHL6.svg)
KMT2C.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|6.47 |
15 14
|BL |Thomas cohort | NA |
16 15
|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |2.90 |
16
+|DLBCL |GAMBL genomes |3.25 |
18 17
|DLBCL |Schmitz cohort |8.30 |
19 18
|DLBCL |Reddy cohort |7.30 |
20 19
|DLBCL |Chapuy cohort |6.40 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |0.628 |0.000 |
27 26
|DLBCL |No |No |1.569 |1.911 |
28 27
|FL |No |No |0.550 |0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Zhou P](https://pubmed.ncbi.nlm.nih.gov/31300419). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Zhou P](https://pubmed.ncbi.nlm.nih.gov/31300419). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2C_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KMT2C_NM_170606.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2C.html)
7
+
8
+![image](../../images/proteinpaint/KMT2C.svg)
KMT2D.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|11.32 |
16 15
|BL |Thomas cohort |14.00 |
17 16
|BL |Panea cohort |15.80 |
18
-|DLBCL |GAMBL genomes |31.40 |
17
+|DLBCL |GAMBL genomes |33.46 |
19 18
|DLBCL |Schmitz cohort |34.50 |
20 19
|DLBCL |Reddy cohort |22.30 |
21 20
|DLBCL |Chapuy cohort |26.10 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes | 0.689 | 13.459 |
29 28
|DLBCL |No |Yes | 3.731 | 104.190 |
30 29
|FL |No |Yes |20.755 |1353.812 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2D_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KMT2D_NM_003482.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2D.html)
7
+
8
+![image](../../images/proteinpaint/KMT2D.svg)
KRAS.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.6 |
14
-|DLBCL |Schmitz cohort|3.6 |
15
-|DLBCL |Reddy cohort |1.7 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort|3.60 |
14
+|DLBCL |Reddy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |27.314 |0 |
23 22
|DLBCL |No |No | 5.336 |0 |
24 23
|FL |No |No | 9.959 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KRAS_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KRAS_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/KRAS_NM_033360.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KRAS.html)
7
+
8
+![image](../../images/proteinpaint/KRAS.svg)
LAMA5.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | 3.2 |
14
-|DLBCL |Schmitz cohort|12.1 |
15
-|DLBCL |Reddy cohort | 4.7 |
16
-|DLBCL |Chapuy cohort | 5.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 3.44 |
13
+|DLBCL |Schmitz cohort|12.10 |
14
+|DLBCL |Reddy cohort | 4.70 |
15
+|DLBCL |Chapuy cohort | 5.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0.000 |
23 22
|DLBCL |No |No |2.765 |4.134 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LAMA5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LAMA5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/LAMA5_NM_005560.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LAMA5.html)
7
+
8
+![image](../../images/proteinpaint/LAMA5.svg)
LAPTM5.md
... ...
@@ -0,0 +1,29 @@
1
+# [LAPTM5]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|5.77 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |Yes |No | 0.000 |34.096 |
19
+|DLBCL |Yes |No | 4.311 |46.640 |
20
+|FL |Yes |Yes |15.566 |93.829 |
21
+
22
+## aSHM regions
23
+
24
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
25
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
26
+|chr1 |31229012 |31232011|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A31229012%2D31232011)|NA |
27
+
28
+> [!NOTE]
29
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
LCOR.md
... ...
@@ -2,24 +2,33 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |0.5 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |6.31 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |0.50 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 |0 |
23 22
|DLBCL |No |No |0 |0 |
24 23
|FL |No |No |0 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LCOR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LCOR_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/LCOR_NM_001346516.svg
30
+images/proteinpaint/LCOR_NM_032440.svg)
31
+
32
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LCOR.html)
33
+
34
+![image](../../images/proteinpaint/LCOR.svg)
LIN54.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|2.1 |
15
-|DLBCL |Reddy cohort |0.9 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|2.10 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.770 | 7.752 |
23 22
|DLBCL |No |No |1.385 |26.297 |
24 23
|FL |No |No |0.000 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LIN54_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LIN54_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/LIN54_NM_194282.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LIN54.html)
7
+
8
+![image](../../images/proteinpaint/LIN54.svg)
LRP12.md
... ...
@@ -0,0 +1,27 @@
1
+# [LRP12]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.217 |7.902 |
22
+|DLBCL |No |No |2.242 |0.000 |
23
+|FL |No |No |1.384 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
LTB.md
... ...
@@ -2,35 +2,43 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
15
-|BL |GAMBL genomes+capture| 3.00 |
16
-|BL |Thomas cohort | 3.00 |
17
-|BL |Panea cohort | 5.90 |
18
-|DLBCL |GAMBL genomes |11.30 |
19
-|DLBCL |Schmitz cohort | 8.50 |
20
-|DLBCL |Reddy cohort | NA |
21
-|DLBCL |Chapuy cohort | 9.80 |
22
-|FL |GAMBL genomes | 8.78 |
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
14
+|BL |GAMBL genomes+capture|3.00 |
15
+|BL |Thomas cohort |3.00 |
16
+|BL |Panea cohort |5.90 |
17
+|DLBCL |GAMBL genomes |9.37 |
18
+|DLBCL |Schmitz cohort |8.50 |
19
+|DLBCL |Reddy cohort | NA |
20
+|DLBCL |Chapuy cohort |9.80 |
21
+|FL |GAMBL genomes |8.78 |
23 22
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |4.330 | 0.000 |
29 28
|DLBCL |Yes |No |2.261 |10.402 |
30 29
|FL |Yes |No |5.259 |35.735 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region |regulatory_comment|
35
-|--------|----------|--------|--------|------------------|
36
-|chr6 |31548325 |31550717|intron-1|enhancer |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:----------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr6 |31548325 |31550717|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A31548325%2D31550717)|enhancer |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LTB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LTB_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/LTB_NM_002341.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LTB.html)
43
+
44
+![image](../../images/proteinpaint/LTB.svg)
LYN.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
14
-|DLBCL |Schmitz cohort|1.7 |
15
-|DLBCL |Reddy cohort |1.3 |
16
-|DLBCL |Chapuy cohort |5.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|1.70 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |5.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No | 1.641 | 0.000 |
23 22
|DLBCL |No |No |10.031 |17.456 |
24 23
|FL |No |No | 0.000 | 0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LYN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LYN_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/LYN_ENST00000519728.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LYN.html)
32
+
33
+![image](../../images/proteinpaint/LYN.svg)
MAGEC1.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.85 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |Yes |26.895 |0.000 |
20 19
|DLBCL |No |No | 1.032 |4.703 |
21 20
|FL |No |No | 0.000 |0.000 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAGEC1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAGEC1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MAGEC1_NM_005462.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAGEC1.html)
7
+
8
+![image](../../images/proteinpaint/MAGEC1.svg)
MAGT1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.6 |
14
-|DLBCL |Schmitz cohort|3.0 |
15
-|DLBCL |Reddy cohort |1.9 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort|3.00 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.329 | 0.000 |
23 22
|DLBCL |No |No |0.000 |57.832 |
24 23
|FL |No |No |0.000 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAGT1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAGT1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MAGT1_NM_032121.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAGT1.html)
7
+
8
+![image](../../images/proteinpaint/MAGT1.svg)
MAP2K1.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |0.70 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |1.34 |
15 14
|DLBCL |Schmitz cohort|3.20 |
16 15
|DLBCL |Reddy cohort |2.20 |
17 16
|DLBCL |Chapuy cohort |2.10 |
... ...
@@ -20,8 +19,17 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No | 4.318 |0 |
25 24
|DLBCL |No |No |11.932 |0 |
26 25
|FL |No |No | 5.696 |0 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP2K1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP2K1_protein_hg38.html)
30
+
31
+![image](../../images/proteinpaint/MAP2K1_NM_002755.svg)
32
+
33
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP2K1.html)
34
+
35
+![image](../../images/proteinpaint/MAP2K1.svg)
MAP3K6.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.54 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.004 |0 |
22 21
|DLBCL |No |No |0.442 |0 |
23 22
|FL |No |No |1.344 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP3K6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP3K6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MAP3K6_NM_004672.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP3K6.html)
7
+
8
+![image](../../images/proteinpaint/MAP3K6.svg)
MAP4K4.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|2.1 |
15
-|DLBCL |Reddy cohort |2.1 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|2.10 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.518 |0.000 |
23 22
|DLBCL |No |No |4.689 |6.978 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP4K4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP4K4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MAP4K4_NM_004834.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP4K4.html)
7
+
8
+![image](../../images/proteinpaint/MAP4K4.svg)
MAP7D1.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
13
-|FL |GAMBL genomes|0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|NA |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.000 |0 |
20 19
|DLBCL |No |No |1.034 |0 |
21 20
|FL |No |No |0.000 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP7D1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP7D1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MAP7D1_NM_018067.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MAP7D1.html)
7
+
8
+![image](../../images/proteinpaint/MAP7D1.svg)
MARK1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|1.9 |
15
-|DLBCL |Reddy cohort |1.3 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.923 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |2.768 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MARK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MARK1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MARK1_NM_018650.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MARK1.html)
7
+
8
+![image](../../images/proteinpaint/MARK1.svg)
MCL1.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|1.85 |
15 14
|BL |Thomas cohort |2.10 |
16 15
|BL |Panea cohort |2.00 |
17
-|DLBCL |GAMBL genomes |2.00 |
16
+|DLBCL |GAMBL genomes |2.49 |
18 17
|DLBCL |Schmitz cohort |3.60 |
19 18
|DLBCL |Reddy cohort |4.70 |
20 19
|DLBCL |Chapuy cohort |3.40 |
... ...
@@ -22,16 +21,24 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |No |5.101 |0.000 |
27 26
|DLBCL |Yes |No |0.427 |2.401 |
28 27
|FL |Yes |No |0.000 |0.000 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
33
-|--------|----------|---------|------|------------------|
34
-|chr1 |150550814 |150552135|intron|NA |
31
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
32
+|:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr1 |150550814 |150552135|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A150550814%2D150552135)|NA |
35 34
36 35
> [!NOTE]
37
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MCL1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MCL1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MCL1_NM_021960.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MCL1.html)
7
+
8
+![image](../../images/proteinpaint/MCL1.svg)
MECOM.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|4.0 |
15 14
|DLBCL |Reddy cohort |2.1 |
16 15
|DLBCL |Chapuy cohort |3.4 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.490 |0 |
23 22
|DLBCL |No |No |1.131 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MECOM_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MECOM_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MECOM_NM_001105077.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MECOM.html)
7
+
8
+![image](../../images/proteinpaint/MECOM.svg)
MEF2B.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 1.39 |
16 15
|BL |Thomas cohort | 0.80 |
17 16
|BL |Panea cohort | 3.00 |
18
-|DLBCL |GAMBL genomes |12.00 |
17
+|DLBCL |GAMBL genomes |11.28 |
19 18
|DLBCL |Schmitz cohort | 9.10 |
20 19
|DLBCL |Reddy cohort | 5.90 |
21 20
|DLBCL |Chapuy cohort | 5.60 |
... ...
@@ -24,13 +23,23 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 2.449 | 0.000 |
29 28
|DLBCL |Yes |Yes | 22.928 |171.945 |
30 29
|FL |Yes |Yes |111.098 | 0.000 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr19 |19279635 |19281441|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr19 |19279635 |19281441|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A19279635%2D19281441)|active_promoter |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2B_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/MEF2B_NM_001145785.svg
41
+images/proteinpaint/MEF2B_zoom.svg)
42
+
43
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2B.html)
44
+
45
+![image](../../images/proteinpaint/MEF2B.svg)
MEF2C.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |3.20 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |3.44 |
15 14
|DLBCL |Schmitz cohort|1.90 |
16 15
|DLBCL |Reddy cohort |1.70 |
17 16
|DLBCL |Chapuy cohort |3.00 |
... ...
@@ -20,15 +19,24 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No | 3.687 | 0.000 |
25 24
|DLBCL |Yes |No | 9.617 |13.957 |
26 25
|FL |Yes |Yes |36.127 | 0.000 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
31
-|--------|----------|--------|------|------------------|
32
-|chr5 |88131209 |88174373|TSS-3 |active_promoter |
33
-|chr5 |88174374 |88182243|TSS-2 |active_promoter |
34
-|chr5 |88182244 |88206620|TSS-1 |active_promoter |
29
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
30
+|:--------:|:----------:|:--------:|:-------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr5 |88131209 |88174373|[TSS-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A88131209%2D88174373)|active_promoter |
32
+|chr5 |88174374 |88182243|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A88174374%2D88182243)|active_promoter |
33
+|chr5 |88182244 |88206620|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A88182244%2D88206620)|active_promoter |
34
+
35
+
36
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2C_protein_hg38.html)
37
+
38
+![image](../../images/proteinpaint/MEF2C_NM_002397.svg)
39
+
40
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2C.html)
41
+
42
+![image](../../images/proteinpaint/MEF2C.svg)
MET.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|3.8 |
15
-|DLBCL |Reddy cohort |1.7 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.76 |
13
+|DLBCL |Schmitz cohort|3.80 |
14
+|DLBCL |Reddy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.327 |0 |
23 22
|DLBCL |No |No |1.141 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MET_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MET_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MET_NM_001127500.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MET.html)
7
+
8
+![image](../../images/proteinpaint/MET.svg)
MGA.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.5 |
14
-|DLBCL |Schmitz cohort|7.2 |
15
-|DLBCL |Reddy cohort |4.7 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.02 |
13
+|DLBCL |Schmitz cohort|7.20 |
14
+|DLBCL |Reddy cohort |4.70 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.443 | 3.733 |
23 22
|DLBCL |No |No |1.432 |12.504 |
24 23
|FL |No |No |0.000 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MGA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MGA_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MGA_NM_001164273.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MGA.html)
7
+
8
+![image](../../images/proteinpaint/MGA.svg)
MGEA5.md
... ...
@@ -0,0 +1,24 @@
1
+# [MGEA5]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|1.85 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.383 |0 |
19
+|DLBCL |No |No |2.152 |0 |
20
+|FL |No |No |3.398 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
MKI67.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|FL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|FL |2 |relevance in FL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|6.00 |
15 14
|BL |Thomas cohort | NA |
16 15
|BL |Panea cohort | NA |
... ...
@@ -19,11 +18,19 @@
19 18
## Mutation pattern
20 19
21 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22
-|------|----|---------------------|----------------|----------------|
21
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23 22
|BL |No |No |1.547 |0 |
24 23
|DLBCL |No |No |1.029 |0 |
25 24
|FL |No |No |0.987 |0 |
26 25
27 26
28 27
> [!NOTE]
29
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MKI67_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MKI67_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MKI67_NM_002417.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MKI67.html)
7
+
8
+![image](../../images/proteinpaint/MKI67.svg)
MME.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort |0.80 |
15 14
|BL |Panea cohort |5.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.702 |0 |
22 21
|DLBCL |No |No |1.177 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MME_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MME_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MME_NM_000902.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MME.html)
7
+
8
+![image](../../images/proteinpaint/MME.svg)
MPEG1.md
... ...
@@ -2,24 +2,30 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | 3.8 |
14
-|DLBCL |Schmitz cohort| 9.1 |
15
-|DLBCL |Reddy cohort | 5.8 |
16
-|DLBCL |Chapuy cohort |10.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 4.78 |
13
+|DLBCL |Schmitz cohort| 9.10 |
14
+|DLBCL |Reddy cohort | 5.80 |
15
+|DLBCL |Chapuy cohort |10.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.434 |0.000 |
23 22
|DLBCL |No |No |1.449 |1.685 |
24 23
|FL |No |No |4.371 |0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPEG1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPEG1_protein_hg38.html)
28
+
29
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPEG1.html)
30
+
31
+![image](../../images/proteinpaint/MPEG1.svg)
MS4A1.md
... ...
@@ -2,29 +2,35 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|1.5 |
15
-|DLBCL |Reddy cohort |1.3 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort|1.50 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |2.434 |29.43 |
23 22
|DLBCL |Yes |No |0.000 | 0.00 |
24 23
|FL |Yes |No |0.000 | 0.00 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr11 |60223385 |60225310|TSS |active_promoter |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr11 |60223385 |60225310|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A60223385%2D60225310)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1_protein_hg38.html)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1.html)
35
+
36
+![image](../../images/proteinpaint/MS4A1.svg)
MSH2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|0.9 |
15
-|DLBCL |Reddy cohort |1.5 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.72 |
13
+|DLBCL |Schmitz cohort|0.90 |
14
+|DLBCL |Reddy cohort |1.50 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.680 |0 |
23 22
|DLBCL |No |No |2.838 |0 |
24 23
|FL |No |No |3.261 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MSH2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MSH2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MSH2_NM_000251.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MSH2.html)
7
+
8
+![image](../../images/proteinpaint/MSH2.svg)
MSH6.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|2.6 |
15
-|DLBCL |Reddy cohort |2.6 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort|2.60 |
14
+|DLBCL |Reddy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.383 |0 |
23 22
|DLBCL |No |No |3.213 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MSH6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MSH6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MSH6_NM_000179.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MSH6.html)
7
+
8
+![image](../../images/proteinpaint/MSH6.svg)
MTOR.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 4.62 |
15 14
|BL |Thomas cohort | 3.40 |
16 15
|BL |Panea cohort |10.90 |
17
-|DLBCL |GAMBL genomes | 4.10 |
16
+|DLBCL |GAMBL genomes | 4.02 |
18 17
|DLBCL |Schmitz cohort | 4.00 |
19 18
|DLBCL |Reddy cohort | 2.40 |
20 19
|DLBCL |Chapuy cohort | 2.10 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |1.204 |0 |
27 26
|DLBCL |No |No |5.630 |0 |
28 27
|FL |No |No |1.429 |0 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MTOR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MTOR_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MTOR_NM_004958.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MTOR.html)
7
+
8
+![image](../../images/proteinpaint/MTOR.svg)
MYB.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.7 |
14
-|DLBCL |Schmitz cohort|2.1 |
15
-|DLBCL |Reddy cohort |1.1 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|2.10 |
14
+|DLBCL |Reddy cohort |1.10 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.555 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |2.377 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYB_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MYB_NM_001130173.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYB.html)
7
+
8
+![image](../../images/proteinpaint/MYB.svg)
MYBPC2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |2.8 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |2.80 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.437 |6.011 |
23 22
|DLBCL |No |No |0.653 |0.000 |
24 23
|FL |No |No |4.460 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYBPC2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYBPC2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MYBPC2_NM_004533.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYBPC2.html)
7
+
8
+![image](../../images/proteinpaint/MYBPC2.svg)
MYC.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|61.89 |
16 15
|BL |Thomas cohort |60.20 |
17 16
|BL |Panea cohort |49.50 |
18
-|DLBCL |GAMBL genomes | 9.90 |
17
+|DLBCL |GAMBL genomes |10.90 |
19 18
|DLBCL |Schmitz cohort | 5.30 |
20 19
|DLBCL |Reddy cohort | 6.20 |
21 20
|DLBCL |Chapuy cohort | 6.40 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |Yes |7.754 |3.964 |
29 28
|DLBCL |Yes |Yes |2.850 |2.582 |
30 29
|FL |Yes |No |4.998 |0.000 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
35
-|--------|----------|---------|------|------------------|
36
-|chr8 |128748352 |128749427|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr8 |128748352 |128749427|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr8%3A128748352%2D128749427)|active_promoter |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYC_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/MYC_NM_002467.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYC.html)
43
+
44
+![image](../../images/proteinpaint/MYC.svg)
MYCBP2.md
... ...
@@ -0,0 +1,24 @@
1
+# [MYCBP2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|3 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.120 |1.153 |
19
+|DLBCL |No |No |0.941 |0.000 |
20
+|FL |No |No |0.850 |7.277 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
MYD88.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 0.46 |
16 15
|BL |Thomas cohort | 0.40 |
17 16
|BL |Panea cohort | 1.00 |
18
-|DLBCL |GAMBL genomes |12.90 |
17
+|DLBCL |GAMBL genomes |13.38 |
19 18
|DLBCL |Schmitz cohort |26.40 |
20 19
|DLBCL |Reddy cohort |15.20 |
21 20
|DLBCL |Chapuy cohort |21.40 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 1.809 |0 |
29 28
|DLBCL |No |Yes |56.390 |0 |
30 29
|FL |No |No |17.159 |0 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYD88_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYD88_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/MYD88_NM_002468.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYD88.html)
38
+
39
+![image](../../images/proteinpaint/MYD88.svg)
MYH10.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.026 |0 |
22 21
|DLBCL |No |No |2.598 |0 |
23 22
|FL |No |No |1.997 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYH10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYH10_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MYH10_NM_005964.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYH10.html)
7
+
8
+![image](../../images/proteinpaint/MYH10.svg)
MYO18A.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.248 |0 |
22 21
|DLBCL |No |No |0.412 |0 |
23 22
|FL |No |No |2.227 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO18A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO18A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/MYO18A_NM_078471.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO18A.html)
7
+
8
+![image](../../images/proteinpaint/MYO18A.svg)
MYO1E.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort |1.30 |
15 14
|BL |Panea cohort |4.00 |
... ...
@@ -17,13 +16,22 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |Yes |No |0.516 |12.845 |
22 21
|DLBCL |Yes |No |0.913 |14.181 |
23 22
|FL |Yes |No |3.818 |29.467 |
24 23
25 24
## aSHM regions
26 25
27
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
28
-|--------|----------|--------|------|------------------|
29
-|chr15 |59658991 |59671152|TSS |NA |
26
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
27
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
28
+|chr15 |59658991 |59671152|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr15%3A59658991%2D59671152)|NA |
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO1E_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO1E_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/MYO1E_NM_004998.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO1E.html)
36
+
37
+![image](../../images/proteinpaint/MYO1E.svg)
MYOM2.md
... ...
@@ -2,24 +2,30 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.6 |
14
-|DLBCL |Schmitz cohort|8.1 |
15
-|DLBCL |Reddy cohort |3.2 |
16
-|DLBCL |Chapuy cohort |4.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.25 |
13
+|DLBCL |Schmitz cohort|8.10 |
14
+|DLBCL |Reddy cohort |3.20 |
15
+|DLBCL |Chapuy cohort |4.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.021 | 0.000 |
23 22
|DLBCL |No |No |0.893 | 2.648 |
24 23
|FL |No |No |0.649 |12.057 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYOM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYOM2_protein_hg38.html)
28
+
29
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYOM2.html)
30
+
31
+![image](../../images/proteinpaint/MYOM2.svg)
N2RF2.md
... ...
@@ -0,0 +1,24 @@
1
+# [N2RF2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+
22
+
23
+> [!NOTE]
24
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
NANOG.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes | NA |
14 13
|DLBCL |Schmitz cohort|0.2 |
15 14
|DLBCL |Reddy cohort |0.4 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 |0 |
23 22
|DLBCL |No |No |0 |0 |
24 23
|FL |No |No |0 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NANOG_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NANOG_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NANOG_NM_024865.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NANOG.html)
7
+
8
+![image](../../images/proteinpaint/NANOG.svg)
NAV1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
14
-|DLBCL |Schmitz cohort|2.8 |
15
-|DLBCL |Reddy cohort |2.0 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Reddy cohort |2.00 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.719 |0 |
23 22
|DLBCL |No |No |0.532 |0 |
24 23
|FL |No |No |1.343 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NAV1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NAV1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NAV1_NM_020443.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NAV1.html)
7
+
8
+![image](../../images/proteinpaint/NAV1.svg)
NBEAL1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.46 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.484 |0.000 |
22 21
|DLBCL |No |No |0.765 |2.824 |
23 22
|FL |No |No |0.863 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NBEAL1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NBEAL1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NBEAL1_NM_001114132.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NBEAL1.html)
7
+
8
+![image](../../images/proteinpaint/NBEAL1.svg)
NCOR1.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|4.5 |
15 14
|DLBCL |Reddy cohort |2.7 |
16 15
|DLBCL |Chapuy cohort |2.1 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.496 |2.331 |
23 22
|DLBCL |No |No |0.935 |4.098 |
24 23
|FL |No |No |1.147 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOR1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOR1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NCOR1_NM_006311.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOR1.html)
7
+
8
+![image](../../images/proteinpaint/NCOR1.svg)
NCOR2.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|6.24 |
15 14
|BL |Thomas cohort | NA |
16 15
|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |2.00 |
16
+|DLBCL |GAMBL genomes |2.10 |
18 17
|DLBCL |Schmitz cohort |5.70 |
19 18
|DLBCL |Reddy cohort |3.60 |
20 19
|DLBCL |Chapuy cohort |4.30 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |0.551 |0.000 |
27 26
|DLBCL |No |No |1.376 |4.613 |
28 27
|FL |No |No |0.985 |0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOR2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOR2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NCOR2_NM_006312.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOR2.html)
7
+
8
+![image](../../images/proteinpaint/NCOR2.svg)
NF1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|4.0 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.87 |
13
+|DLBCL |Schmitz cohort|4.00 |
14
+|DLBCL |Reddy cohort |2.50 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.485 |0.000 |
23 22
|DLBCL |No |No |1.135 |2.469 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NF1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NF1_NM_000267.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NF1.html)
7
+
8
+![image](../../images/proteinpaint/NF1.svg)
NFKB1.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|1.3 |
15 14
|DLBCL |Reddy cohort |1.6 |
16 15
|DLBCL |Chapuy cohort |3.4 |
... ...
@@ -18,8 +17,17 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.644 |0 |
23 22
|DLBCL |No |No |1.613 |0 |
24 23
|FL |No |No |4.561 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKB1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKB1_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/NFKB1_NM_003998.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKB1.html)
32
+
33
+![image](../../images/proteinpaint/NFKB1.svg)
NFKB2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|1.5 |
15
-|DLBCL |Reddy cohort |1.4 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort|1.50 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.937 |0.00 |
23 22
|DLBCL |No |No |0.861 |8.02 |
24 23
|FL |No |No |2.873 |0.00 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKB2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NFKB2_NM_001077494.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKB2.html)
7
+
8
+![image](../../images/proteinpaint/NFKB2.svg)
NFKBIA.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|1.39 |
16 15
|BL |Thomas cohort |1.70 |
17 16
|BL |Panea cohort |2.00 |
18
-|DLBCL |GAMBL genomes |4.10 |
17
+|DLBCL |GAMBL genomes |4.40 |
19 18
|DLBCL |Schmitz cohort |3.80 |
20 19
|DLBCL |Reddy cohort |3.60 |
21 20
|DLBCL |Chapuy cohort |4.70 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |3.358 |17.442 |
29 28
|DLBCL |No |Yes |9.385 |40.878 |
30 29
|FL |No |No |0.000 |28.519 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIA_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/NFKBIA_NM_020529.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIA.html)
38
+
39
+![image](../../images/proteinpaint/NFKBIA.svg)
NFKBIE.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.3 |
14
-|DLBCL |Schmitz cohort|5.7 |
15
-|DLBCL |Reddy cohort |2.9 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|5.70 |
14
+|DLBCL |Reddy cohort |2.90 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.702 | 0.000 |
23 22
|DLBCL |No |Yes |8.732 |58.269 |
24 23
|FL |No |No |0.000 |46.628 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2016 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/26647218)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2016 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/26647218)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIE_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIE_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NFKBIE_NM_004556.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIE.html)
7
+
8
+![image](../../images/proteinpaint/NFKBIE.svg)
NFKBIZ.md
... ...
@@ -2,30 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort |1.5 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort |1.50 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |3.346 |0 |
23 22
|DLBCL |Yes |No |2.091 |0 |
24 23
|FL |Yes |No |0.000 |0 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
29
-|--------|----------|---------|------|------------------|
30
-|chr3 |101546669 |101547704|TSS-1 |active_promoter |
31
-|chr3 |101568239 |101569274|TSS-2 |active_promoter |
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:---------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr3 |101546669 |101547704|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A101546669%2D101547704)|active_promoter |
30
+|chr3 |101568239 |101569274|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A101568239%2D101569274)|active_promoter |
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIZ_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIZ_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/NFKBIZ_zoom.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIZ.html)
38
+
39
+![image](../../images/proteinpaint/NFKBIZ.svg)
NLRC5.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|8.3 |
15
-|DLBCL |Reddy cohort |3.7 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.06 |
13
+|DLBCL |Schmitz cohort|8.30 |
14
+|DLBCL |Reddy cohort |3.70 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.602 | 0.000 |
23 22
|DLBCL |No |No |0.529 |20.155 |
24 23
|FL |No |No |0.000 | 7.677 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRC5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRC5_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/NLRC5_NM_032206.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRC5.html)
32
+
33
+![image](../../images/proteinpaint/NLRC5.svg)
NLRP8.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |2.1 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.456 |7.316 |
23 22
|DLBCL |No |No |2.731 |0.000 |
24 23
|FL |No |No |0.000 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP8_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NLRP8_NM_176811.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP8.html)
7
+
8
+![image](../../images/proteinpaint/NLRP8.svg)
NOA1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.31 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.647 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOA1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOA1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NOA1_NM_032313.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOA1.html)
7
+
8
+![image](../../images/proteinpaint/NOA1.svg)
NOL9.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.7 |
14
-|DLBCL |Schmitz cohort|6.8 |
15
-|DLBCL |Reddy cohort |1.3 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.97 |
13
+|DLBCL |Schmitz cohort|6.80 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.514 |0 |
23 22
|DLBCL |No |No |4.012 |0 |
24 23
|FL |No |No |2.619 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOL9_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOL9_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/NOL9_NM_024654.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOL9.html)
32
+
33
+![image](../../images/proteinpaint/NOL9.svg)
NOTCH1.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|4.16 |
15 14
|BL |Thomas cohort | NA |
16 15
|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |2.50 |
16
+|DLBCL |GAMBL genomes |3.44 |
18 17
|DLBCL |Schmitz cohort |8.90 |
19 18
|DLBCL |Reddy cohort |3.40 |
20 19
|DLBCL |Chapuy cohort |3.00 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |1.031 |0 |
27 26
|DLBCL |No |No |0.792 |0 |
28 27
|FL |No |No |2.864 |0 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOTCH1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOTCH1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NOTCH1_NM_017617.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOTCH1.html)
7
+
8
+![image](../../images/proteinpaint/NOTCH1.svg)
NOTCH2.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 1.15 |
15 14
|BL |Thomas cohort | 0.00 |
16 15
|BL |Panea cohort | 5.00 |
17
-|DLBCL |GAMBL genomes | 6.80 |
16
+|DLBCL |GAMBL genomes | 5.74 |
18 17
|DLBCL |Schmitz cohort |11.30 |
19 18
|DLBCL |Reddy cohort | 3.70 |
20 19
|DLBCL |Chapuy cohort | 7.30 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |0.000 | 0.000 |
27 26
|DLBCL |No |Yes |0.527 |60.245 |
28 27
|FL |No |No |0.000 | 0.000 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOTCH2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOTCH2_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/NOTCH2_NM_024408.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NOTCH2.html)
36
+
37
+![image](../../images/proteinpaint/NOTCH2.svg)
NRXN2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.77 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.039 |0 |
22 21
|DLBCL |No |No |1.624 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NRXN2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NRXN2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/NRXN2_NM_015080.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NRXN2.html)
7
+
8
+![image](../../images/proteinpaint/NRXN2.svg)
OR8H2.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.15 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.795 |0 |
20 19
|DLBCL |No |No |0.000 |0 |
21 20
|FL |No |No |7.647 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OR8H2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OR8H2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/OR8H2_NM_001005200.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OR8H2.html)
7
+
8
+![image](../../images/proteinpaint/OR8H2.svg)
OSBPL10.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 2.08 |
15 14
|BL |Thomas cohort | 2.10 |
16 15
|BL |Panea cohort | 3.00 |
... ...
@@ -22,13 +21,22 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |No | 4.102 |11.721 |
27 26
|DLBCL |Yes |Yes |12.983 | 0.000 |
28 27
|FL |Yes |Yes | 5.877 | 8.779 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
33
-|--------|----------|--------|------|------------------|
34
-|chr3 |32020518 |32024930|TSS-1 |active_promoter |
31
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
32
+|:--------:|:----------:|:--------:|:-------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr3 |32020518 |32024930|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A32020518%2D32024930)|active_promoter |
34
+
35
+
36
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OSBPL10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OSBPL10_protein_hg38.html)
37
+
38
+![image](../../images/proteinpaint/OSBPL10_NM_017784.svg)
39
+
40
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OSBPL10.html)
41
+
42
+![image](../../images/proteinpaint/OSBPL10.svg)
P2RY2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.15 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.862 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RY2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RY2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/P2RY2_NM_176072.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RY2.html)
7
+
8
+![image](../../images/proteinpaint/P2RY2.svg)
P2RY8.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 6.93 |
16 15
|BL |Thomas cohort |11.00 |
17 16
|BL |Panea cohort | NA |
18
-|DLBCL |GAMBL genomes | 7.20 |
17
+|DLBCL |GAMBL genomes | 6.88 |
19 18
|DLBCL |Schmitz cohort | 7.20 |
20 19
|DLBCL |Reddy cohort | NA |
21 20
|DLBCL |Chapuy cohort | 6.00 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |58.153 |189.145 |
29 28
|DLBCL |No |Yes |31.041 | 0.000 |
30 29
|FL |No |No |23.117 | 0.000 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
... ...
\ No newline at end of file
0
+> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RY8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RY8_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/P2RY8_NM_178129.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RY8.html)
7
+
8
+![image](../../images/proteinpaint/P2RY8.svg)
PABPC4L.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort |1.30 |
15 14
|BL |Panea cohort |3.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.776 |0 |
22 21
|DLBCL |No |No |2.948 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PABPC4L_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PABPC4L_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PABPC4L_NM_001114734.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PABPC4L.html)
7
+
8
+![image](../../images/proteinpaint/PABPC4L.svg)
PAPOLG.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.2 |
14
-|DLBCL |Schmitz cohort|0.9 |
15
-|DLBCL |Reddy cohort |1.2 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|0.90 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |1.554 |0 |
24 23
|FL |No |No |4.497 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PAPOLG_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PAPOLG_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PAPOLG_NM_022894.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PAPOLG.html)
7
+
8
+![image](../../images/proteinpaint/PAPOLG.svg)
PAX5.md
... ...
@@ -2,36 +2,43 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.5 |
14
-|DLBCL |Schmitz cohort|3.2 |
15
-|DLBCL |Reddy cohort |1.9 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.63 |
13
+|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No | 6.750 |0 |
23 22
|DLBCL |Yes |Yes |14.089 |0 |
24 23
|FL |Yes |No |10.963 |0 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region |regulatory_comment|
29
-|--------|----------|--------|-----------------|------------------|
30
-|chr9 |37023396 |37027663|intron-1 |intron |
31
-|chr9 |37029849 |37037154|TSS-1 |active_promoter |
32
-|chr9 |37369209 |37372160|distal-enhancer-1|enhancer |
33
-|chr9 |37382267 |37385854|distal-enhancer-2|enhancer |
34
-|chr9 |37395932 |37409239|distal-enhancer-3|enhancer |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-------------------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr9 |37023396 |37027663|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37023396%2D37027663) |intron |
30
+|chr9 |37029849 |37037154|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37029849%2D37037154) |active_promoter |
31
+|chr9 |37369209 |37372160|[distal-enhancer-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37369209%2D37372160)|enhancer |
32
+|chr9 |37382267 |37385854|[distal-enhancer-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37382267%2D37385854)|enhancer |
33
+|chr9 |37395932 |37409239|[distal-enhancer-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37395932%2D37409239)|enhancer |
35 34
36 35
> [!NOTE]
37
-> First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PAX5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PAX5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PAX5_NM_016734.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PAX5.html)
7
+
8
+![image](../../images/proteinpaint/PAX5.svg)
PC.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.54 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.187 | 0.000 |
22 21
|DLBCL |No |No |0.000 |10.914 |
23 22
|FL |No |No |0.000 |27.654 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PC_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PC_NM_000920.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PC.html)
7
+
8
+![image](../../images/proteinpaint/PC.svg)
PCBP1.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|12.24 |
15 14
|BL |Thomas cohort |12.30 |
16 15
|BL |Panea cohort |11.90 |
17
-|DLBCL |GAMBL genomes | 1.60 |
16
+|DLBCL |GAMBL genomes | 1.34 |
18 17
|DLBCL |Schmitz cohort | 2.30 |
19 18
|DLBCL |Reddy cohort | 2.40 |
20 19
|DLBCL |Chapuy cohort | 1.70 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |16.780 |424.685 |
27 26
|DLBCL |No |No | 0.000 | 0.000 |
28 27
|FL |No |No | 1.401 | 0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2015 by [Wagener R](https://pubmed.ncbi.nlm.nih.gov/26173642)
... ...
\ No newline at end of file
0
+> First described in BL in 2015 by [Wagener R](https://pubmed.ncbi.nlm.nih.gov/26173642)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCBP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCBP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PCBP1_NM_006196.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCBP1.html)
7
+
8
+![image](../../images/proteinpaint/PCBP1.svg)
PCDHA11.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort |1.30 |
15 14
|BL |Panea cohort |3.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.171 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.784 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHA11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHA11_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PCDHA11_NM_018902.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHA11.html)
7
+
8
+![image](../../images/proteinpaint/PCDHA11.svg)
PCLO.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |15.30 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |16.44 |
15 14
|DLBCL |Schmitz cohort|21.30 |
16 15
|DLBCL |Reddy cohort |15.10 |
17 16
|DLBCL |Chapuy cohort |23.10 |
... ...
@@ -20,11 +19,19 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |0.000 |0.000 |
25 24
|DLBCL |No |No |1.223 |0.389 |
26 25
|FL |No |No |0.000 |0.000 |
27 26
28 27
29 28
> [!NOTE]
30
-> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCLO_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCLO_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PCLO_NM_033026.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCLO.html)
7
+
8
+![image](../../images/proteinpaint/PCLO.svg)
PDCD11.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.46 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |4.985 |0 |
22 21
|DLBCL |No |No |2.400 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDCD11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDCD11_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PDCD11_NM_014976.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDCD11.html)
7
+
8
+![image](../../images/proteinpaint/PDCD11.svg)
PDE4DIP.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | NA |
14 13
|DLBCL |Schmitz cohort|2.3 |
15 14
|DLBCL |Reddy cohort |5.3 |
16 15
|DLBCL |Chapuy cohort |8.5 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.344 |1.032 |
23 22
|DLBCL |No |No |1.467 |5.897 |
24 23
|FL |No |No |2.010 |7.866 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDE4DIP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDE4DIP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PDE4DIP_NM_014644.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDE4DIP.html)
7
+
8
+![image](../../images/proteinpaint/PDE4DIP.svg)
PDS5B.md
... ...
@@ -0,0 +1,24 @@
1
+# [PDS5B]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|1.62 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.009 |2.705 |
19
+|DLBCL |No |No |1.333 |6.726 |
20
+|FL |No |No |0.000 |9.065 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
PDZRN3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.46 |
14 13
|BL |Thomas cohort |2.10 |
15 14
|BL |Panea cohort |9.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.623 |0 |
22 21
|DLBCL |No |No |0.461 |0 |
23 22
|FL |No |No |0.935 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDZRN3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDZRN3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PDZRN3_NM_015009.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDZRN3.html)
7
+
8
+![image](../../images/proteinpaint/PDZRN3.svg)
PHF6.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|7.16 |
15 14
|BL |Thomas cohort |5.50 |
16 15
|BL |Panea cohort |5.90 |
17
-|DLBCL |GAMBL genomes |2.30 |
16
+|DLBCL |GAMBL genomes |2.49 |
18 17
|DLBCL |Schmitz cohort |1.50 |
19 18
|DLBCL |Reddy cohort |1.40 |
20 19
|DLBCL |Chapuy cohort |0.90 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |10.853 |196.689 |
27 26
|DLBCL |No |No | 6.130 | 36.559 |
28 27
|FL |No |No |31.614 | 0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PHF6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PHF6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PHF6_NM_001015877.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PHF6.html)
7
+
8
+![image](../../images/proteinpaint/PHF6.svg)
PIK3CD.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.1 |
14
-|DLBCL |Schmitz cohort|4.9 |
15
-|DLBCL |Reddy cohort |2.5 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|4.90 |
14
+|DLBCL |Reddy cohort |2.50 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |4.941 |0 |
23 22
|DLBCL |No |No |4.970 |0 |
24 23
|FL |No |No |5.721 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIK3CD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIK3CD_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/PIK3CD_NM_005026.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIK3CD.html)
32
+
33
+![image](../../images/proteinpaint/PIK3CD.svg)
PIK3R1.md
... ...
@@ -2,31 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
14
-|BL |GAMBL genomes+capture|3.0 |
15
-|BL |Thomas cohort |2.5 |
16
-|BL |Panea cohort |4.0 |
17
-|DLBCL |GAMBL genomes |2.0 |
18
-|DLBCL |Schmitz cohort |2.1 |
19
-|DLBCL |Reddy cohort |2.0 |
20
-|DLBCL |Chapuy cohort |4.7 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture|3.00 |
14
+|BL |Thomas cohort |2.50 |
15
+|BL |Panea cohort |4.00 |
16
+|DLBCL |GAMBL genomes |1.91 |
17
+|DLBCL |Schmitz cohort |2.10 |
18
+|DLBCL |Reddy cohort |2.00 |
19
+|DLBCL |Chapuy cohort |4.70 |
21 20
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |3.917 | 0.000 |
27 26
|DLBCL |No |No |2.158 |16.154 |
28 27
|FL |No |No |0.000 |14.389 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIK3R1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIK3R1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PIK3R1_NM_181523.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIK3R1.html)
7
+
8
+![image](../../images/proteinpaint/PIK3R1.svg)
PIM1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 2.31 |
16 15
|BL |Thomas cohort | NA |
17 16
|BL |Panea cohort | NA |
18
-|DLBCL |GAMBL genomes |18.50 |
17
+|DLBCL |GAMBL genomes |20.27 |
19 18
|DLBCL |Schmitz cohort |27.70 |
20 19
|DLBCL |Reddy cohort |19.10 |
21 20
|DLBCL |Chapuy cohort |23.90 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No |6.021 |0.000 |
29 28
|DLBCL |Yes |Yes |2.096 |2.418 |
30 29
|FL |Yes |No |4.214 |0.000 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr6 |37138104 |37139804|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
35
+|chr6 |37138104 |37139804|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A37138104%2D37139804)|active_promoter |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PIM1_NM_002648.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM1.html)
7
+
8
+![image](../../images/proteinpaint/PIM1.svg)
PIM2.md
... ...
@@ -2,29 +2,37 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|6.4 |
15
-|DLBCL |Reddy cohort |4.0 |
16
-|DLBCL |Chapuy cohort |3.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.44 |
13
+|DLBCL |Schmitz cohort|6.40 |
14
+|DLBCL |Reddy cohort |4.00 |
15
+|DLBCL |Chapuy cohort |3.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |0.000 | 0.000 |
23 22
|DLBCL |Yes |No |1.908 |14.378 |
24 23
|FL |Yes |No |0.000 |62.405 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chrX |48774756 |48776255|TSS |active_promoter |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29
+|chrX |48774756 |48776255|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A48774756%2D48776255)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM2_protein_hg38.html)
33
+
34
+![image](../../images/proteinpaint/PIM2_NM_006875.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM2.html)
37
+
38
+![image](../../images/proteinpaint/PIM2.svg)
PLCG2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture| 3.0 |
14 13
|BL |Thomas cohort | 0.8 |
15 14
|BL |Panea cohort |10.9 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.800 | 0.000 |
22 21
|DLBCL |No |No |2.213 |14.094 |
23 22
|FL |No |No |1.491 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLCG2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLCG2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PLCG2_NM_002661.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLCG2.html)
7
+
8
+![image](../../images/proteinpaint/PLCG2.svg)
PMAIP1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.23 |
14 13
|BL |Thomas cohort |3.00 |
15 14
|BL |Panea cohort |5.00 |
... ...
@@ -17,8 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |Yes |15.382 |90.742 |
22 21
|DLBCL |No |No | 0.000 | 0.000 |
23 22
|FL |No |No | 0.000 | 0.000 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PMAIP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PMAIP1_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/PMAIP1_NM_021127.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PMAIP1.html)
31
+
32
+![image](../../images/proteinpaint/PMAIP1.svg)
PNPO.md
... ...
@@ -0,0 +1,27 @@
1
+# [PNPO]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.503 |0 |
22
+|DLBCL |No |No |4.698 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
POLRMT.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.969 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POLRMT_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POLRMT_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/POLRMT_NM_005035.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POLRMT.html)
7
+
8
+![image](../../images/proteinpaint/POLRMT.svg)
POR.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.54 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.005 |0 |
22 21
|DLBCL |No |No |1.464 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POR_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/POR_NM_001382657.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POR.html)
7
+
8
+![image](../../images/proteinpaint/POR.svg)
POU2AF1.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes | 5.00 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes | 5.16 |
15 14
|DLBCL |Schmitz cohort| 2.30 |
16 15
|DLBCL |Reddy cohort | 3.30 |
17 16
|DLBCL |Chapuy cohort | 5.60 |
... ...
@@ -20,13 +19,22 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |Yes |No |0.000 | 0.000 |
25 24
|DLBCL |Yes |No |6.798 | 74.689 |
26 25
|FL |Yes |Yes |0.000 |659.924 |
27 26
28 27
## aSHM regions
29 28
30
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
31
-|--------|----------|---------|------|------------------|
32
-|chr11 |111248078 |111250224|TSS |active_promoter |
29
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
30
+|:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr11 |111248078 |111250224|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A111248078%2D111250224)|active_promoter |
32
+
33
+
34
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POU2AF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POU2AF1_protein_hg38.html)
35
+
36
+![image](../../images/proteinpaint/POU2AF1_NM_006235.svg)
37
+
38
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POU2AF1.html)
39
+
40
+![image](../../images/proteinpaint/POU2AF1.svg)
POU2F2.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |5.20 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |5.93 |
15 14
|DLBCL |Schmitz cohort|6.40 |
16 15
|DLBCL |Reddy cohort |3.40 |
17 16
|DLBCL |Chapuy cohort |6.40 |
... ...
@@ -20,8 +19,17 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No | 3.431 | 0.000 |
25 24
|DLBCL |No |Yes |12.445 |51.943 |
26 25
|FL |No |No |17.646 | 0.000 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POU2F2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POU2F2_protein_hg38.html)
30
+
31
+![image](../../images/proteinpaint/POU2F2_NM_002698.svg)
32
+
33
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POU2F2.html)
34
+
35
+![image](../../images/proteinpaint/POU2F2.svg)
PPP1R9B.md
... ...
@@ -2,24 +2,30 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |0.7 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.267 |10.265 |
23 22
|DLBCL |No |No |0.632 | 0.000 |
24 23
|FL |No |No |0.000 |34.824 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B_protein_hg38.html)
28
+
29
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B.html)
30
+
31
+![image](../../images/proteinpaint/PPP1R9B.svg)
PPP4C.md
... ...
@@ -0,0 +1,24 @@
1
+# [PPP4C]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|2.08 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No | 2.143 |25.647 |
19
+|DLBCL |No |No | 6.715 | 0.000 |
20
+|FL |No |No |43.394 | 0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
PPP6R2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.193 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP6R2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP6R2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PPP6R2_NM_014678.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP6R2.html)
7
+
8
+![image](../../images/proteinpaint/PPP6R2.svg)
PRDM1.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 2.31 |
15 14
|BL |Thomas cohort | 0.80 |
16 15
|BL |Panea cohort | 5.90 |
17
-|DLBCL |GAMBL genomes | 8.10 |
16
+|DLBCL |GAMBL genomes | 6.88 |
18 17
|DLBCL |Schmitz cohort |10.20 |
19 18
|DLBCL |Reddy cohort | 5.40 |
20 19
|DLBCL |Chapuy cohort | 8.50 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |0.746 | 0.000 |
27 26
|DLBCL |No |Yes |4.912 |23.497 |
28 27
|FL |No |No |0.000 | 0.000 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRDM1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRDM1_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/PRDM1_NM_001198.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRDM1.html)
36
+
37
+![image](../../images/proteinpaint/PRDM1.svg)
PREX1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.633 | 4.023 |
22 21
|DLBCL |No |No |0.722 | 4.039 |
23 22
|FL |No |No |1.695 |10.067 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PREX1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PREX1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PREX1_NM_020820.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PREX1.html)
7
+
8
+![image](../../images/proteinpaint/PREX1.svg)
PRKCB.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.3 |
14
-|DLBCL |Schmitz cohort|5.1 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.97 |
13
+|DLBCL |Schmitz cohort|5.10 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |3.889 |0 |
24 23
|FL |No |No |1.828 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCB_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/PRKCB_NM_212535.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCB.html)
32
+
33
+![image](../../images/proteinpaint/PRKCB.svg)
PRKCD.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.31 |
14 13
|BL |Thomas cohort |1.30 |
15 14
|BL |Panea cohort |5.90 |
... ...
@@ -17,8 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No | 2.225 | 0.000 |
22 21
|DLBCL |No |Yes |11.290 |71.966 |
23 22
|FL |No |No |25.696 | 0.000 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCD_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/PRKCD_NM_006254.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCD.html)
31
+
32
+![image](../../images/proteinpaint/PRKCD.svg)
PRKDC.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene |
8
+|FL |2 |relevance in FL not firmly established|
9 9
## Mutation incidence
10 10
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.9 |
14
-|DLBCL |Schmitz cohort|7.7 |
15
-|DLBCL |Reddy cohort |6.6 |
16
-|DLBCL |Chapuy cohort |6.4 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |2.68 |
14
+|DLBCL |Schmitz cohort|7.70 |
15
+|DLBCL |Reddy cohort |6.60 |
16
+|DLBCL |Chapuy cohort |6.40 |
17
+|FL |GAMBL genomes |3.00 |
17 18
18 19
## Mutation pattern
19 20
20 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 23
|BL |No |No |0.571 |0.939 |
23 24
|DLBCL |No |No |1.076 |0.000 |
24 25
|FL |No |No |0.000 |7.794 |
25 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKDC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKDC_protein_hg38.html)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKDC.html)
32
+
33
+![image](../../images/proteinpaint/PRKDC.svg)
PRPS1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|0.6 |
15
-|DLBCL |Reddy cohort |0.2 |
16
-|DLBCL |Chapuy cohort |0.9 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.76 |
13
+|DLBCL |Schmitz cohort|0.60 |
14
+|DLBCL |Reddy cohort |0.20 |
15
+|DLBCL |Chapuy cohort |0.90 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |3.078 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRPS1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRPS1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PRPS1_NM_002764.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRPS1.html)
7
+
8
+![image](../../images/proteinpaint/PRPS1.svg)
PRSS22.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.023 |0 |
22 21
|DLBCL |No |No |2.370 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRSS22_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRSS22_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PRSS22_NM_022119.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRSS22.html)
7
+
8
+![image](../../images/proteinpaint/PRSS22.svg)
PTEN.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|4.16 |
15 14
|BL |Thomas cohort |4.70 |
16 15
|BL |Panea cohort |4.00 |
17
-|DLBCL |GAMBL genomes |3.20 |
16
+|DLBCL |GAMBL genomes |3.82 |
18 17
|DLBCL |Schmitz cohort |4.30 |
19 18
|DLBCL |Reddy cohort |3.10 |
20 19
|DLBCL |Chapuy cohort |4.70 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |22.104 |81.225 |
27 26
|DLBCL |No |No | 4.548 |76.677 |
28 27
|FL |No |No | 4.634 | 0.000 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTEN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTEN_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/PTEN_NM_000314.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTEN.html)
36
+
37
+![image](../../images/proteinpaint/PTEN.svg)
PTPN6.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|4.5 |
15
-|DLBCL |Reddy cohort |2.9 |
16
-|DLBCL |Chapuy cohort |5.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|4.50 |
14
+|DLBCL |Reddy cohort |2.90 |
15
+|DLBCL |Chapuy cohort |5.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 | 0.000 |
23 22
|DLBCL |No |No |5.433 |14.931 |
24 23
|FL |No |No |0.000 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PTPN6_NM_002831.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN6.html)
7
+
8
+![image](../../images/proteinpaint/PTPN6.svg)
PTPRD.md
... ...
@@ -2,26 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |4.7 |
15
-|DLBCL |Schmitz cohort|7.7 |
16
-|DLBCL |Reddy cohort |5.2 |
17
-|DLBCL |Chapuy cohort |5.6 |
18
-|FL |GAMBL genomes |3.7 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |5.54 |
14
+|DLBCL |Schmitz cohort|7.70 |
15
+|DLBCL |Reddy cohort |5.20 |
16
+|DLBCL |Chapuy cohort |5.60 |
17
+|FL |GAMBL genomes |3.70 |
19 18
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |1.905 |0.000 |
25 24
|DLBCL |No |No |0.969 |0.000 |
26 25
|FL |No |No |1.549 |3.769 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRD_protein_hg38.html)
30
+
31
+![image](../../images/proteinpaint/PTPRD_NM_002839.svg)
32
+
33
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRD.html)
34
+
35
+![image](../../images/proteinpaint/PTPRD.svg)
PTPRK.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.1 |
14
-|DLBCL |Schmitz cohort|3.6 |
15
-|DLBCL |Reddy cohort |3.3 |
16
-|DLBCL |Chapuy cohort |6.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.21 |
13
+|DLBCL |Schmitz cohort|3.60 |
14
+|DLBCL |Reddy cohort |3.30 |
15
+|DLBCL |Chapuy cohort |6.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.146 |0.000 |
23 22
|DLBCL |No |No |1.555 |1.797 |
24 23
|FL |No |No |1.875 |5.021 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRK_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PTPRK_NM_001135648.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRK.html)
7
+
8
+![image](../../images/proteinpaint/PTPRK.svg)
PTPRN.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.69 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0 |0 |
22 21
|DLBCL |No |No |0 |0 |
23 22
|FL |No |No |0 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRN_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PTPRN_NM_002846.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPRN.html)
7
+
8
+![image](../../images/proteinpaint/PTPRN.svg)
PXDNL.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.62 |
14 13
|BL |Thomas cohort |3.00 |
15 14
|BL |Panea cohort |9.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.255 |0 |
22 21
|DLBCL |No |No |1.924 |0 |
23 22
|FL |No |No |1.165 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PXDNL_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PXDNL_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PXDNL_NM_144651.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PXDNL.html)
7
+
8
+![image](../../images/proteinpaint/PXDNL.svg)
PZP.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.92 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.936 |0 |
20 19
|DLBCL |No |No |0.273 |0 |
21 20
|FL |No |No |1.723 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PZP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PZP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/PZP_NM_002864.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PZP.html)
7
+
8
+![image](../../images/proteinpaint/PZP.svg)
RAC2.md
... ...
@@ -2,26 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 9
## Mutation incidence
10 10
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13 13
|BL |GAMBL genomes+capture|0.69 |
14 14
|BL |Thomas cohort |0.40 |
15 15
|BL |Panea cohort | NA |
16
+|DLBCL |GAMBL genomes |1.15 |
17
+|DLBCL |Schmitz cohort | NA |
18
+|DLBCL |Reddy cohort | NA |
19
+|DLBCL |Chapuy cohort | NA |
16 20
17 21
## Mutation pattern
18 22
19 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 25
|BL |No |No |9.926 |0 |
22 26
|DLBCL |No |No |6.256 |0 |
23 27
|FL |No |No |0.000 |0 |
24 28
25 29
26 30
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RAC2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RAC2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RAC2_NM_002872.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RAC2.html)
7
+
8
+![image](../../images/proteinpaint/RAC2.svg)
RAD9A.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | NA |
14
-|DLBCL |Schmitz cohort|0.4 |
15
-|DLBCL |Reddy cohort |0.5 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|0.40 |
14
+|DLBCL |Reddy cohort |0.50 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 |0 |
23 22
|DLBCL |No |No |0 |0 |
24 23
|FL |No |No |0 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RAD9A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RAD9A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RAD9A_NM_004584.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RAD9A.html)
7
+
8
+![image](../../images/proteinpaint/RAD9A.svg)
RANBP6.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |3.815 |0 |
22 21
|DLBCL |No |No |0.306 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RANBP6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RANBP6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RANBP6_NM_012416.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RANBP6.html)
7
+
8
+![image](../../images/proteinpaint/RANBP6.svg)
RARA.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|4.0 |
15
-|DLBCL |Reddy cohort |0.7 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|4.00 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |6.208 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RARA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RARA_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RARA_NM_000964.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RARA.html)
7
+
8
+![image](../../images/proteinpaint/RARA.svg)
RB1.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.6 |
14
-|DLBCL |Schmitz cohort|3.2 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort |3.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.78 |
13
+|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |3.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.029 | 6.855 |
23 22
|DLBCL |No |Yes |0.933 |17.514 |
24 23
|FL |No |No |1.890 | 0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RB1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RB1_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/RB1_NM_000321.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RB1.html)
32
+
33
+![image](../../images/proteinpaint/RB1.svg)
RBM6.md
... ...
@@ -0,0 +1,24 @@
1
+# [RBM6]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|0.46 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.85 |0 |
19
+|DLBCL |No |No |0.00 |0 |
20
+|FL |No |No |0.00 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
RBP3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.69 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.00 |0 |
22 21
|DLBCL |No |No |0.38 |0 |
23 22
|FL |No |No |0.00 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RBP3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RBP3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RBP3_NM_002900.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RBP3.html)
7
+
8
+![image](../../images/proteinpaint/RBP3.svg)
RET.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.31 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.901 |0 |
22 21
|DLBCL |No |No |2.518 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RET_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RET_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RET_NM_020630.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RET.html)
7
+
8
+![image](../../images/proteinpaint/RET.svg)
REV3L.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.067 |0 |
22 21
|DLBCL |No |No |0.915 |0 |
23 22
|FL |No |No |0.731 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/REV3L_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/REV3L_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/REV3L_NM_002912.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/REV3L.html)
7
+
8
+![image](../../images/proteinpaint/REV3L.svg)
RFX7.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|9.47 |
15 14
|BL |Thomas cohort |9.30 |
16 15
|BL |Panea cohort |4.00 |
17
-|DLBCL |GAMBL genomes |3.20 |
16
+|DLBCL |GAMBL genomes |4.02 |
18 17
|DLBCL |Schmitz cohort |1.90 |
19 18
|DLBCL |Reddy cohort |3.40 |
20 19
|DLBCL |Chapuy cohort |4.70 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |2.347 |98.419 |
27 26
|DLBCL |No |No |1.219 |17.441 |
28 27
|FL |No |No |0.000 | 0.000 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFX7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFX7_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/RFX7_NM_022841.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFX7.html)
36
+
37
+![image](../../images/proteinpaint/RFX7.svg)
RFXAP.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort |0.6 |
16
-|DLBCL |Chapuy cohort | NA |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort |0.60 |
15
+|DLBCL |Chapuy cohort | NA |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.222 |91.553 |
23 22
|DLBCL |No |No |3.462 |29.787 |
24 23
|FL |No |No |4.119 | 0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFXAP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFXAP_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/RFXAP_NM_000538.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFXAP.html)
32
+
33
+![image](../../images/proteinpaint/RFXAP.svg)
RHOA.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 9.47 |
15 14
|BL |Thomas cohort | 8.10 |
16 15
|BL |Panea cohort |12.90 |
17
-|DLBCL |GAMBL genomes | 3.20 |
16
+|DLBCL |GAMBL genomes | 3.06 |
18 17
|DLBCL |Schmitz cohort | 3.60 |
19 18
|DLBCL |Reddy cohort | 3.30 |
20 19
|DLBCL |Chapuy cohort | 5.10 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |88.993 |0 |
27 26
|DLBCL |No |Yes |52.294 |0 |
28 27
|FL |No |No |31.528 |0 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOA_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/RHOA_NM_001664.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOA.html)
36
+
37
+![image](../../images/proteinpaint/RHOA.svg)
RNF144B.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.23 |
14 13
|BL |Thomas cohort |0.40 |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,16 +16,24 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |Yes |No |0 |0 |
22 21
|DLBCL |Yes |No |0 |0 |
23 22
|FL |Yes |No |0 |0 |
24 23
25 24
## aSHM regions
26 25
27
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
28
-|--------|----------|--------|------|------------------|
29
-|chr6 |25861094 |25868788|TSS |NA |
26
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
27
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
28
+|chr6 |25861094 |25868788|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A25861094%2D25868788)|NA |
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RNF144B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RNF144B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RNF144B_NM_182757.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RNF144B.html)
7
+
8
+![image](../../images/proteinpaint/RNF144B.svg)
RPL10.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|13.63 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.00 |0 |
22 21
|DLBCL |No |No |1.03 |0 |
23 22
|FL |No |No |0.00 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL10_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RPL10_NM_006013.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL10.html)
7
+
8
+![image](../../images/proteinpaint/RPL10.svg)
RPL22.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.31 |
14 13
|BL |Thomas cohort |3.00 |
15 14
|BL |Panea cohort |2.00 |
... ...
@@ -17,8 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |Yes |16.054 |60.122 |
22 21
|DLBCL |No |No | 0.000 | 0.000 |
23 22
|FL |No |No |21.073 | 0.000 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL22_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL22_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/RPL22_NM_000983.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL22.html)
31
+
32
+![image](../../images/proteinpaint/RPL22.svg)
RRAGC.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
8
+|FL |1 |high-confidence FL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes | 1.80 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes | 1.72 |
15 14
|DLBCL |Schmitz cohort| 3.00 |
16 15
|DLBCL |Reddy cohort | 2.00 |
17 16
|DLBCL |Chapuy cohort | 0.40 |
... ...
@@ -20,11 +19,19 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No | 0.000 |0 |
25 24
|DLBCL |No |No | 2.679 |0 |
26 25
|FL |No |Yes |163.715 |0 |
27 26
28 27
29 28
> [!NOTE]
30
-> First described in DLBCL in 2016 by [Okosun J](https://pubmed.ncbi.nlm.nih.gov/26691987)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2016 by [Okosun J](https://pubmed.ncbi.nlm.nih.gov/26691987)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RRAGC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RRAGC_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RRAGC_NM_022157.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RRAGC.html)
7
+
8
+![image](../../images/proteinpaint/RRAGC.svg)
RUNX1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|0.9 |
15
-|DLBCL |Reddy cohort |0.5 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|0.90 |
14
+|DLBCL |Reddy cohort |0.50 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0 |0 |
23 22
|DLBCL |No |No |0 |0 |
24 23
|FL |No |No |0 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RUNX1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RUNX1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/RUNX1_NM_001754.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RUNX1.html)
7
+
8
+![image](../../images/proteinpaint/RUNX1.svg)
S1PR2.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|1.15 |
16 15
|BL |Thomas cohort |0.00 |
17 16
|BL |Panea cohort |4.00 |
18
-|DLBCL |GAMBL genomes |4.10 |
17
+|DLBCL |GAMBL genomes |4.78 |
19 18
|DLBCL |Schmitz cohort |2.10 |
20 19
|DLBCL |Reddy cohort |2.20 |
21 20
|DLBCL |Chapuy cohort |2.60 |
... ...
@@ -24,16 +23,24 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 0.000 | 0.000 |
29 28
|DLBCL |Yes |Yes |34.147 | 0.000 |
30 29
|FL |Yes |Yes |36.780 |339.679 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chr19 |10340142 |10341764|TSS |active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr19 |10340142 |10341764|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A10340142%2D10341764)|active_promoter |
37 36
38 37
> [!NOTE]
39
-> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307)
... ...
\ No newline at end of file
0
+> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/S1PR2_NM_004230.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR2.html)
7
+
8
+![image](../../images/proteinpaint/S1PR2.svg)
SAL3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,8 +16,14 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAL3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAL3_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAL3.html)
5
+
6
+![image](../../images/proteinpaint/SAL3.svg)
SALL3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.16 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.641 | 0.000 |
22 21
|DLBCL |No |No |1.052 |13.148 |
23 22
|FL |No |No |1.660 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SALL3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SALL3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SALL3_NM_171999.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SALL3.html)
7
+
8
+![image](../../images/proteinpaint/SALL3.svg)
SAPS2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|NA |
14 13
|BL |Thomas cohort |NA |
15 14
|BL |Panea cohort |NA |
... ...
@@ -17,8 +16,14 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAPS2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAPS2_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAPS2.html)
5
+
6
+![image](../../images/proteinpaint/SAPS2.svg)
SBF1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|4.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.613 | 0.000 |
22 21
|DLBCL |No |No |2.003 |12.038 |
23 22
|FL |No |No |1.554 |19.971 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SBF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SBF1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SBF1_NM_002972.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SBF1.html)
7
+
8
+![image](../../images/proteinpaint/SBF1.svg)
SEPT10.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.92 |
14 13
|BL |Thomas cohort |2.10 |
15 14
|BL |Panea cohort |2.00 |
... ...
@@ -17,8 +16,17 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |7.224 |13.447 |
22 21
|DLBCL |No |No |0.000 | 0.000 |
23 22
|FL |No |No |2.834 | 0.000 |
24 23
24
+
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEPT10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEPT10_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/SEPT10_NM_144710.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEPT10.html)
31
+
32
+![image](../../images/proteinpaint/SEPT10.svg)
SESN1.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|0.23 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |4.805 |0 |
20 19
|DLBCL |No |No |1.629 |0 |
21 20
|FL |No |No |0.000 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2017 by [Oricchio E](https://pubmed.ncbi.nlm.nih.gov/28659443)
... ...
\ No newline at end of file
0
+> First described in FL in 2017 by [Oricchio E](https://pubmed.ncbi.nlm.nih.gov/28659443)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SESN1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SESN1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SESN1_NM_014454.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SESN1.html)
7
+
8
+![image](../../images/proteinpaint/SESN1.svg)
SETD1B.md
... ...
@@ -2,24 +2,30 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | 3.6 |
14
-|DLBCL |Schmitz cohort|12.8 |
15
-|DLBCL |Reddy cohort | 5.8 |
16
-|DLBCL |Chapuy cohort | NA |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 5.16 |
13
+|DLBCL |Schmitz cohort|12.80 |
14
+|DLBCL |Reddy cohort | 5.80 |
15
+|DLBCL |Chapuy cohort | NA |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 | 0.000 |
23 22
|DLBCL |No |No |2.645 | 24.278 |
24 23
|FL |No |Yes |4.979 |128.132 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD1B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD1B_protein_hg38.html)
28
+
29
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD1B.html)
30
+
31
+![image](../../images/proteinpaint/SETD1B.svg)
SETD2.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|6.4 |
15
-|DLBCL |Reddy cohort |4.6 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.63 |
13
+|DLBCL |Schmitz cohort|6.40 |
14
+|DLBCL |Reddy cohort |4.60 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.730 |0 |
23 22
|DLBCL |No |No |2.572 |0 |
24 23
|FL |No |No |2.306 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD2_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/SETD2_NM_014159.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD2.html)
32
+
33
+![image](../../images/proteinpaint/SETD2.svg)
SETD5.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.5 |
14
-|DLBCL |Schmitz cohort|5.3 |
15
-|DLBCL |Reddy cohort |3.2 |
16
-|DLBCL |Chapuy cohort |2.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|5.30 |
14
+|DLBCL |Reddy cohort |3.20 |
15
+|DLBCL |Chapuy cohort |2.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 | 0.000 |
23 22
|DLBCL |No |No |0.841 |32.108 |
24 23
|FL |No |No |2.236 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SETD5_NM_001080517.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD5.html)
7
+
8
+![image](../../images/proteinpaint/SETD5.svg)
SF3B1.md
... ...
@@ -2,31 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
14
-|BL |GAMBL genomes+capture|3.0 |
15
-|BL |Thomas cohort | NA |
16
-|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |2.0 |
18
-|DLBCL |Schmitz cohort |2.1 |
19
-|DLBCL |Reddy cohort |2.0 |
20
-|DLBCL |Chapuy cohort |3.0 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture|3.00 |
14
+|BL |Thomas cohort | NA |
15
+|BL |Panea cohort | NA |
16
+|DLBCL |GAMBL genomes |2.87 |
17
+|DLBCL |Schmitz cohort |2.10 |
18
+|DLBCL |Reddy cohort |2.00 |
19
+|DLBCL |Chapuy cohort |3.00 |
21 20
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |2.277 |0.000 |
27 26
|DLBCL |No |No |3.245 |7.004 |
28 27
|FL |No |No |2.408 |0.000 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SF3B1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SF3B1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SF3B1_NM_012433.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SF3B1.html)
7
+
8
+![image](../../images/proteinpaint/SF3B1.svg)
SGK1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 2.08 |
16 15
|BL |Thomas cohort | 2.50 |
17 16
|BL |Panea cohort | 4.00 |
18
-|DLBCL |GAMBL genomes |11.70 |
17
+|DLBCL |GAMBL genomes |11.09 |
19 18
|DLBCL |Schmitz cohort |10.60 |
20 19
|DLBCL |Reddy cohort |11.20 |
21 20
|DLBCL |Chapuy cohort |12.80 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 5.451 | 7.487 |
29 28
|DLBCL |Yes |Yes | 6.056 | 13.755 |
30 29
|FL |Yes |Yes |23.198 |134.356 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end |region|regulatory_comment|
35
-|--------|----------|---------|------|------------------|
36
-|chr6 |134487960 |134499859|TSS-1 |active_promoter |
33
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
34
+|:--------:|:----------:|:---------:|:---------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr6 |134487960 |134499859|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A134487960%2D134499859)|active_promoter |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SGK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SGK1_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/SGK1_NM_005627.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SGK1.html)
43
+
44
+![image](../../images/proteinpaint/SGK1.svg)
SHANK1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.77 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.869 |0 |
22 21
|DLBCL |No |No |0.895 |0 |
23 22
|FL |No |No |2.138 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SHANK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SHANK1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SHANK1_NM_016148.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SHANK1.html)
7
+
8
+![image](../../images/proteinpaint/SHANK1.svg)
SHROOM3.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.15 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.333 |0 |
20 19
|DLBCL |No |No |1.125 |0 |
21 20
|FL |No |No |0.774 |0 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SHROOM3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SHROOM3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SHROOM3_NM_020859.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SHROOM3.html)
7
+
8
+![image](../../images/proteinpaint/SHROOM3.svg)
SIAH2.md
... ...
@@ -0,0 +1,27 @@
1
+# [SIAH2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.72 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.000 |0 |
22
+|DLBCL |No |No |9.796 |0 |
23
+|FL |No |No |4.227 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
SIN3A.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|11.09 |
15 14
|BL |Thomas cohort |10.60 |
16 15
|BL |Panea cohort |14.90 |
17
-|DLBCL |GAMBL genomes | 2.90 |
16
+|DLBCL |GAMBL genomes | 3.06 |
18 17
|DLBCL |Schmitz cohort | 2.80 |
19 18
|DLBCL |Reddy cohort | 3.00 |
20 19
|DLBCL |Chapuy cohort | 3.80 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |3.871 |55.210 |
27 26
|DLBCL |No |No |2.483 |15.818 |
28 27
|FL |No |No |0.000 |20.676 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SIN3A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SIN3A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SIN3A_NM_001145358.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SIN3A.html)
7
+
8
+![image](../../images/proteinpaint/SIN3A.svg)
SLC29A2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.46 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0 |0 |
22 21
|DLBCL |No |No |0 |0 |
23 22
|FL |No |No |0 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SLC29A2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SLC29A2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SLC29A2_NM_001532.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SLC29A2.html)
7
+
8
+![image](../../images/proteinpaint/SLC29A2.svg)
SLC34A2.md
... ...
@@ -0,0 +1,27 @@
1
+# [SLC34A2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.76 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |3.011 |0 |
22
+|DLBCL |No |No |1.526 |0 |
23
+|FL |No |No |1.687 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
SMARCA4.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|22.63 |
16 15
|BL |Thomas cohort |17.80 |
17 16
|BL |Panea cohort |18.80 |
18
-|DLBCL |GAMBL genomes | 2.70 |
17
+|DLBCL |GAMBL genomes | 3.25 |
19 18
|DLBCL |Schmitz cohort | 3.00 |
20 19
|DLBCL |Reddy cohort | 3.30 |
21 20
|DLBCL |Chapuy cohort | 2.10 |
... ...
@@ -24,11 +23,19 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |13.014 |7.632 |
29 28
|DLBCL |No |No | 3.876 |0.000 |
30 29
|FL |No |No |11.081 |0.000 |
31 30
32 31
33 32
> [!NOTE]
34
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCA4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCA4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SMARCA4_NM_001128849.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCA4.html)
7
+
8
+![image](../../images/proteinpaint/SMARCA4.svg)
SMEK1.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | NA |
14 13
|DLBCL |Schmitz cohort| NA |
15 14
|DLBCL |Reddy cohort |0.9 |
16 15
|DLBCL |Chapuy cohort |3.0 |
... ...
@@ -18,11 +17,17 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 | 5.691 |
23 22
|DLBCL |No |No |1.264 | 0.000 |
24 23
|FL |No |No |9.566 |58.730 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMEK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMEK1_protein_hg38.html)
3
+
4
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMEK1.html)
5
+
6
+![image](../../images/proteinpaint/SMEK1.svg)
SNTB2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.69 |
14 13
|BL |Thomas cohort |0.00 |
15 14
|BL |Panea cohort |2.00 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |3.904 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SNTB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SNTB2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SNTB2_NM_006750.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SNTB2.html)
7
+
8
+![image](../../images/proteinpaint/SNTB2.svg)
SOCS1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 1.85 |
16 15
|BL |Thomas cohort | 1.70 |
17 16
|BL |Panea cohort | 3.00 |
18
-|DLBCL |GAMBL genomes |16.50 |
17
+|DLBCL |GAMBL genomes |15.30 |
19 18
|DLBCL |Schmitz cohort |12.80 |
20 19
|DLBCL |Reddy cohort |10.40 |
21 20
|DLBCL |Chapuy cohort | 4.70 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 4.476 | 0.000 |
29 28
|DLBCL |Yes |Yes | 5.023 | 17.509 |
30 29
|FL |Yes |Yes |21.460 |123.344 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region |regulatory_comment|
35
-|--------|----------|--------|--------|------------------|
36
-|chr16 |11347512 |11350007|intron-1|enhancer |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------------:|:------------------:|
35
+|chr16 |11347512 |11350007|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A11347512%2D11350007)|enhancer |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SOCS1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SOCS1_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/SOCS1_NM_003745.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SOCS1.html)
43
+
44
+![image](../../images/proteinpaint/SOCS1.svg)
SP3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.0 |
14 13
|BL |Thomas cohort |2.5 |
15 14
|BL |Panea cohort |5.0 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.249 |16.244 |
22 21
|DLBCL |No |No |1.085 |25.775 |
23 22
|FL |No |No |2.231 |27.201 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SP3_NM_003111.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP3.html)
7
+
8
+![image](../../images/proteinpaint/SP3.svg)
SPEN.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | 3.4 |
14
-|DLBCL |Schmitz cohort|10.0 |
15
-|DLBCL |Reddy cohort | 7.4 |
16
-|DLBCL |Chapuy cohort | 9.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 4.78 |
13
+|DLBCL |Schmitz cohort|10.00 |
14
+|DLBCL |Reddy cohort | 7.40 |
15
+|DLBCL |Chapuy cohort | 9.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.456 | 0.000 |
23 22
|DLBCL |No |No |0.900 |13.083 |
24 23
|FL |No |No |1.765 |25.228 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SPEN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SPEN_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/SPEN_NM_015001.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SPEN.html)
32
+
33
+![image](../../images/proteinpaint/SPEN.svg)
SRRM2.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|1.39 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |1.604 |1.723 |
20 19
|DLBCL |No |No |1.835 |0.000 |
21 20
|FL |No |No |1.461 |0.000 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SRRM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SRRM2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SRRM2_NM_016333.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SRRM2.html)
7
+
8
+![image](../../images/proteinpaint/SRRM2.svg)
STAB2.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|2.54 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.371 |1.052 |
20 19
|DLBCL |No |No |0.781 |0.000 |
21 20
|FL |No |No |1.912 |0.000 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAB2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/STAB2_NM_017564.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAB2.html)
7
+
8
+![image](../../images/proteinpaint/STAB2.svg)
STAT3.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|0.92 |
15 14
|BL |Thomas cohort |0.00 |
16 15
|BL |Panea cohort |1.00 |
17
-|DLBCL |GAMBL genomes |7.40 |
16
+|DLBCL |GAMBL genomes |7.07 |
18 17
|DLBCL |Schmitz cohort |9.40 |
19 18
|DLBCL |Reddy cohort |3.60 |
20 19
|DLBCL |Chapuy cohort |7.30 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No | 0.000 | 0.000 |
27 26
|DLBCL |No |Yes |27.471 |12.427 |
28 27
|FL |No |No |34.737 | 0.000 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT3_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/STAT3_NM_139276.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT3.html)
36
+
37
+![image](../../images/proteinpaint/STAT3.svg)
STAT5B.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|0.4 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|0.40 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.137 |0 |
23 22
|DLBCL |No |No |1.568 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT5B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT5B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/STAT5B_NM_012448.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT5B.html)
7
+
8
+![image](../../images/proteinpaint/STAT5B.svg)
STAT6.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 1.62 |
16 15
|BL |Thomas cohort | 1.70 |
17 16
|BL |Panea cohort | 2.00 |
18
-|DLBCL |GAMBL genomes | 4.50 |
17
+|DLBCL |GAMBL genomes | 5.74 |
19 18
|DLBCL |Schmitz cohort | 2.60 |
20 19
|DLBCL |Reddy cohort | 3.80 |
21 20
|DLBCL |Chapuy cohort | 4.70 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 3.301 |0 |
29 28
|DLBCL |No |No | 11.582 |0 |
30 29
|FL |No |Yes |116.612 |0 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT6_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/STAT6_NM_003153.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/STAT6.html)
38
+
39
+![image](../../images/proteinpaint/STAT6.svg)
SYK.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|2.3 |
15
-|DLBCL |Reddy cohort |0.8 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort|2.30 |
14
+|DLBCL |Reddy cohort |0.80 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |2.281 | 0.00 |
23 22
|DLBCL |No |No |3.818 |12.94 |
24 23
|FL |No |No |0.000 | 0.00 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYK_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SYK_NM_003177.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYK.html)
7
+
8
+![image](../../images/proteinpaint/SYK.svg)
SYNCRIP.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|3.0 |
14 13
|BL |Thomas cohort |2.5 |
15 14
|BL |Panea cohort |5.0 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No | 4.806 |35.301 |
22 21
|DLBCL |No |No | 2.325 |47.239 |
23 22
|FL |No |No |16.820 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNCRIP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNCRIP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SYNCRIP_NM_006372.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNCRIP.html)
7
+
8
+![image](../../images/proteinpaint/SYNCRIP.svg)
SYNGAP1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.39 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.464 |0 |
22 21
|DLBCL |No |No |0.650 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNGAP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNGAP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/SYNGAP1_NM_006772.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNGAP1.html)
7
+
8
+![image](../../images/proteinpaint/SYNGAP1.svg)
TAF1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |5.4 |
14
-|DLBCL |Schmitz cohort|4.9 |
15
-|DLBCL |Reddy cohort |4.0 |
16
-|DLBCL |Chapuy cohort |3.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.78 |
13
+|DLBCL |Schmitz cohort|4.90 |
14
+|DLBCL |Reddy cohort |4.00 |
15
+|DLBCL |Chapuy cohort |3.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.410 |0 |
23 22
|DLBCL |No |No |5.884 |0 |
24 23
|FL |No |No |8.661 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAF1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TAF1_NM_004606.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAF1.html)
7
+
8
+![image](../../images/proteinpaint/TAF1.svg)
TAP1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|3.6 |
15
-|DLBCL |Reddy cohort | NA |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|3.60 |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.986 | 0.000 |
23 22
|DLBCL |No |No |0.632 | 0.000 |
24 23
|FL |No |No |3.142 |39.164 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TAP1_NM_000593.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAP1.html)
7
+
8
+![image](../../images/proteinpaint/TAP1.svg)
TBC1D9B.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |2.926 |0.000 |
22 21
|DLBCL |No |No |0.871 |9.918 |
23 22
|FL |No |No |0.000 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D9B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D9B_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TBC1D9B_NM_198868.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D9B.html)
7
+
8
+![image](../../images/proteinpaint/TBC1D9B.svg)
TBL1XR1.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 6.00 |
16 15
|BL |Thomas cohort | 4.70 |
17 16
|BL |Panea cohort | 7.90 |
18
-|DLBCL |GAMBL genomes | 8.80 |
17
+|DLBCL |GAMBL genomes | 8.60 |
19 18
|DLBCL |Schmitz cohort |12.80 |
20 19
|DLBCL |Reddy cohort | 5.70 |
21 20
|DLBCL |Chapuy cohort | 8.10 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes |17.892 |29.577 |
29 28
|DLBCL |No |Yes |24.811 |24.179 |
30 29
|FL |No |No |12.400 |18.940 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBL1XR1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBL1XR1_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/TBL1XR1_NM_024665.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBL1XR1.html)
38
+
39
+![image](../../images/proteinpaint/TBL1XR1.svg)
TCF3.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|BL |1 |high-confidence BL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|11.55 |
14 13
|BL |Thomas cohort |11.00 |
15 14
|BL |Panea cohort | 9.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |4.463 |34.108 |
22 21
|DLBCL |No |No |1.567 | 0.000 |
23 22
|FL |No |No |0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TCF3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TCF3_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TCF3_NM_003200.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TCF3.html)
7
+
8
+![image](../../images/proteinpaint/TCF3.svg)
TCL1A.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|4.16 |
15 14
|BL |Thomas cohort |5.90 |
16 15
|BL |Panea cohort |4.00 |
17
-|DLBCL |GAMBL genomes |2.00 |
16
+|DLBCL |GAMBL genomes |2.10 |
18 17
|DLBCL |Schmitz cohort |3.80 |
19 18
|DLBCL |Reddy cohort |2.80 |
20 19
|DLBCL |Chapuy cohort |3.00 |
... ...
@@ -22,16 +21,24 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |Yes |13.813 | 49.800 |
27 26
|DLBCL |Yes |Yes |25.501 |112.487 |
28 27
|FL |Yes |No |30.159 | 88.355 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
33
-|--------|----------|--------|------|------------------|
34
-|chr14 |96179535 |96180366|TSS |active_promoter |
31
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
32
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr14 |96179535 |96180366|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr14%3A96179535%2D96180366)|active_promoter |
35 34
36 35
> [!NOTE]
37
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TCL1A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TCL1A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TCL1A_NM_021966.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TCL1A.html)
7
+
8
+![image](../../images/proteinpaint/TCL1A.svg)
TET2.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture| 5.31 |
15 14
|BL |Thomas cohort | 5.10 |
16 15
|BL |Panea cohort |10.90 |
17
-|DLBCL |GAMBL genomes | 6.30 |
16
+|DLBCL |GAMBL genomes | 5.54 |
18 17
|DLBCL |Schmitz cohort |11.70 |
19 18
|DLBCL |Reddy cohort | 7.40 |
20 19
|DLBCL |Chapuy cohort | 6.00 |
... ...
@@ -22,11 +21,19 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |1.516 |25.932 |
27 26
|DLBCL |No |Yes |0.663 |12.181 |
28 27
|FL |No |No |0.892 |10.949 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TET2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TET2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TET2_NM_001127208.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TET2.html)
7
+
8
+![image](../../images/proteinpaint/TET2.svg)
TFAP4.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|BL |1 |high-confidence BL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|10.16 |
14 13
|BL |Thomas cohort |10.60 |
15 14
|BL |Panea cohort | 9.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |Yes |16.997 |47.948 |
22 21
|DLBCL |No |No | 5.215 | 0.000 |
23 22
|FL |No |No | 0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TFAP4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TFAP4_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TFAP4_NM_003223.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TFAP4.html)
7
+
8
+![image](../../images/proteinpaint/TFAP4.svg)
TGFBR2.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|1.9 |
15 14
|DLBCL |Reddy cohort |1.9 |
16 15
|DLBCL |Chapuy cohort |1.3 |
... ...
@@ -18,11 +17,19 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.941 |0.000 |
23 22
|DLBCL |No |No |0.599 |8.085 |
24 23
|FL |No |No |2.530 |0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TGFBR2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TGFBR2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TGFBR2_NM_001024847.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TGFBR2.html)
7
+
8
+![image](../../images/proteinpaint/TGFBR2.svg)
TIGD6.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.15 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |4.838 |0 |
22 21
|DLBCL |No |No |0.000 |0 |
23 22
|FL |No |No |4.007 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIGD6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIGD6_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TIGD6_NM_030953.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIGD6.html)
7
+
8
+![image](../../images/proteinpaint/TIGD6.svg)
TIPARP.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes | NA |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort |0.9 |
16
-|DLBCL |Chapuy cohort | NA |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort | NA |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.495 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIPARP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIPARP_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TIPARP_NM_015508.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIPARP.html)
7
+
8
+![image](../../images/proteinpaint/TIPARP.svg)
TLR2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |2.7 |
14
-|DLBCL |Schmitz cohort|2.8 |
15
-|DLBCL |Reddy cohort |1.5 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.87 |
13
+|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Reddy cohort |1.50 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.141 |0 |
23 22
|DLBCL |No |No |3.705 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TLR2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TLR2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TLR2_NM_003264.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TLR2.html)
7
+
8
+![image](../../images/proteinpaint/TLR2.svg)
TMEM30A.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |2 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |2 |relevance in FL not firmly established|
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|1.85 |
16 15
|BL |Thomas cohort |1.30 |
17 16
|BL |Panea cohort |5.00 |
18
-|DLBCL |GAMBL genomes |5.00 |
17
+|DLBCL |GAMBL genomes |4.78 |
19 18
|DLBCL |Schmitz cohort |7.70 |
20 19
|DLBCL |Reddy cohort |2.80 |
21 20
|DLBCL |Chapuy cohort |5.60 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |4.270 | 46.360 |
29 28
|DLBCL |No |Yes |0.000 |221.848 |
30 29
|FL |No |No |5.098 | 0.000 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMEM30A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMEM30A_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/TMEM30A_NM_018247.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMEM30A.html)
38
+
39
+![image](../../images/proteinpaint/TMEM30A.svg)
TMSB4X.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 0.69 |
16 15
|BL |Thomas cohort | 0.00 |
17 16
|BL |Panea cohort | 2.00 |
18
-|DLBCL |GAMBL genomes |14.40 |
17
+|DLBCL |GAMBL genomes |12.43 |
19 18
|DLBCL |Schmitz cohort |18.10 |
20 19
|DLBCL |Reddy cohort |13.10 |
21 20
|DLBCL |Chapuy cohort |18.40 |
... ...
@@ -24,13 +23,22 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |Yes |No | 0.000 | 0.000 |
29 28
|DLBCL |Yes |Yes |23.522 |254.537 |
30 29
|FL |Yes |Yes |60.545 |310.498 |
31 30
32 31
## aSHM regions
33 32
34
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
35
-|--------|----------|--------|------|------------------|
36
-|chrX |12993308 |12994511|intron|active_promoter |
33
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
34
+|:--------:|:----------:|:--------:|:--------------------------------------------------------------------------------------------:|:------------------:|
35
+|chrX |12993308 |12994511|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A12993308%2D12994511)|active_promoter |
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMSB4X_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMSB4X_protein_hg38.html)
39
+
40
+![image](../../images/proteinpaint/TMSB4X_NM_021109.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMSB4X.html)
43
+
44
+![image](../../images/proteinpaint/TMSB4X.svg)
TNFAIP3.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 1.39 |
16 15
|BL |Thomas cohort | 0.80 |
17 16
|BL |Panea cohort | 2.00 |
18
-|DLBCL |GAMBL genomes | 6.10 |
17
+|DLBCL |GAMBL genomes | 6.69 |
19 18
|DLBCL |Schmitz cohort |16.60 |
20 19
|DLBCL |Reddy cohort | 8.10 |
21 20
|DLBCL |Chapuy cohort |12.40 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No |1.168 |16.846 |
29 28
|DLBCL |No |Yes |1.550 |30.319 |
30 29
|FL |No |No |5.686 |75.953 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TNFAIP3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TNFAIP3_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/TNFAIP3_NM_006290.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TNFAIP3.html)
38
+
39
+![image](../../images/proteinpaint/TNFAIP3.svg)
TNFRSF14.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture| 1.39 |
16 15
|BL |Thomas cohort | 0.80 |
17 16
|BL |Panea cohort | 3.00 |
18
-|DLBCL |GAMBL genomes |14.20 |
17
+|DLBCL |GAMBL genomes |14.34 |
19 18
|DLBCL |Schmitz cohort |16.80 |
20 19
|DLBCL |Reddy cohort | 9.70 |
21 20
|DLBCL |Chapuy cohort |12.80 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |No | 1.388 | 34.410 |
29 28
|DLBCL |No |Yes |32.541 | 207.456 |
30 29
|FL |No |Yes |96.380 |1034.281 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TNFRSF14_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TNFRSF14_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/TNFRSF14_NM_003820.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TNFRSF14.html)
38
+
39
+![image](../../images/proteinpaint/TNFRSF14.svg)
TOP2A.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |3.194 |0 |
22 21
|DLBCL |No |No |0.774 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TOP2A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TOP2A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TOP2A_NM_001067.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TOP2A.html)
7
+
8
+![image](../../images/proteinpaint/TOP2A.svg)
TOX.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|2.08 |
15 14
|BL |Thomas cohort |0.80 |
16 15
|BL |Panea cohort |5.90 |
17
-|DLBCL |GAMBL genomes |4.50 |
16
+|DLBCL |GAMBL genomes |4.21 |
18 17
|DLBCL |Schmitz cohort |5.50 |
19 18
|DLBCL |Reddy cohort |4.00 |
20 19
|DLBCL |Chapuy cohort |5.10 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |1.503 |17.955 |
27 26
|DLBCL |No |No |3.481 |12.292 |
28 27
|FL |No |No |1.975 |21.081 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TOX_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TOX_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/TOX_NM_014729.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TOX.html)
36
+
37
+![image](../../images/proteinpaint/TOX.svg)
TP53.md
... ...
@@ -2,20 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-|FL |1 |
10
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
9
+|FL |1 |high-confidence FL gene |
11 10
## Mutation incidence
12 11
13
-|Entity|study |frequency (%)|
14
-|------|---------------------|-------------|
12
+|Entity|source |frequency (%)|
13
+|:------:|:---------------------:|:-------------:|
15 14
|BL |GAMBL genomes+capture|45.50 |
16 15
|BL |Thomas cohort |41.90 |
17 16
|BL |Panea cohort |43.60 |
18
-|DLBCL |GAMBL genomes |21.90 |
17
+|DLBCL |GAMBL genomes |27.53 |
19 18
|DLBCL |Schmitz cohort |22.30 |
20 19
|DLBCL |Reddy cohort |10.90 |
21 20
|DLBCL |Chapuy cohort |21.40 |
... ...
@@ -24,8 +23,17 @@
24 23
## Mutation pattern
25 24
26 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27
-|------|----|---------------------|----------------|----------------|
26
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
28 27
|BL |No |Yes | 83.783 | 58.309 |
29 28
|DLBCL |No |Yes |127.531 |143.760 |
30 29
|FL |No |Yes | 63.211 |142.226 |
31 30
31
+
32
+
33
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TP53_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TP53_protein_hg38.html)
34
+
35
+![image](../../images/proteinpaint/TP53_NM_000546.svg)
36
+
37
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TP53.html)
38
+
39
+![image](../../images/proteinpaint/TP53.svg)
TPP1.md
... ...
@@ -0,0 +1,24 @@
1
+# [TPP1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|FL |GAMBL genomes|0.92 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.831 | 0.000 |
19
+|DLBCL |No |No |0.969 | 0.000 |
20
+|FL |No |No |9.163 |29.516 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
TPST2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.92 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.788 |0 |
22 21
|DLBCL |No |No |2.633 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TPST2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TPST2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TPST2_NM_001008566.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TPST2.html)
7
+
8
+![image](../../images/proteinpaint/TPST2.svg)
TRAF3.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|1.5 |
15
-|DLBCL |Reddy cohort |0.9 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|1.50 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.795 |0 |
23 22
|DLBCL |No |No |1.440 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRAF3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRAF3_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/TRAF3_NM_145725.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRAF3.html)
32
+
33
+![image](../../images/proteinpaint/TRAF3.svg)
TRAF6.md
... ...
@@ -0,0 +1,27 @@
1
+# [TRAF6]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.000 | 0.000 |
22
+|DLBCL |No |No |1.970 |61.299 |
23
+|FL |No |No |9.831 | 0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
TRIP12.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.2 |
14
-|DLBCL |Schmitz cohort|6.0 |
15
-|DLBCL |Reddy cohort |3.2 |
16
-|DLBCL |Chapuy cohort |3.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.25 |
13
+|DLBCL |Schmitz cohort|6.00 |
14
+|DLBCL |Reddy cohort |3.20 |
15
+|DLBCL |Chapuy cohort |3.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.620 |0 |
23 22
|DLBCL |No |No |1.161 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRIP12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRIP12_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/TRIP12_NM_004238.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRIP12.html)
32
+
33
+![image](../../images/proteinpaint/TRIP12.svg)
TRRAP.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.2 |
14
-|DLBCL |Schmitz cohort|8.9 |
15
-|DLBCL |Reddy cohort |3.5 |
16
-|DLBCL |Chapuy cohort |6.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.87 |
13
+|DLBCL |Schmitz cohort|8.90 |
14
+|DLBCL |Reddy cohort |3.50 |
15
+|DLBCL |Chapuy cohort |6.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.571 |0 |
23 22
|DLBCL |No |No |1.296 |0 |
24 23
|FL |No |No |2.757 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRRAP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRRAP_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/TRRAP_NM_003496.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRRAP.html)
32
+
33
+![image](../../images/proteinpaint/TRRAP.svg)
TTN.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|28.64 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 |0.000 |
22 21
|DLBCL |No |No |0.921 |1.537 |
23 22
|FL |No |No |0.000 |0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TTN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TTN_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/TTN_NM_133378.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TTN.html)
7
+
8
+![image](../../images/proteinpaint/TTN.svg)
UBE2A.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|0.92 |
15 14
|BL |Thomas cohort |0.00 |
16 15
|BL |Panea cohort |3.00 |
17
-|DLBCL |GAMBL genomes |3.40 |
16
+|DLBCL |GAMBL genomes |4.21 |
18 17
|DLBCL |Schmitz cohort |7.00 |
19 18
|DLBCL |Reddy cohort |3.90 |
20 19
|DLBCL |Chapuy cohort |4.70 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No | 0.000 |0 |
27 26
|DLBCL |No |Yes |26.609 |0 |
28 27
|FL |No |No |51.360 |0 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2A_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/UBE2A_NM_003336.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2A.html)
36
+
37
+![image](../../images/proteinpaint/UBE2A.svg)
UBR5.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.4 |
14
-|DLBCL |Schmitz cohort|5.5 |
15
-|DLBCL |Reddy cohort |3.2 |
16
-|DLBCL |Chapuy cohort |5.1 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.63 |
13
+|DLBCL |Schmitz cohort|5.50 |
14
+|DLBCL |Reddy cohort |3.20 |
15
+|DLBCL |Chapuy cohort |5.10 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.678 |1.875 |
23 22
|DLBCL |No |No |1.342 |5.285 |
24 23
|FL |No |No |0.918 |6.988 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBR5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBR5_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/UBR5_NM_015902.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBR5.html)
7
+
8
+![image](../../images/proteinpaint/UBR5.svg)
UNC5B.md
... ...
@@ -0,0 +1,27 @@
1
+# [UNC5B]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.517 |0 |
22
+|DLBCL |No |No |2.632 |0 |
23
+|FL |No |No |4.218 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
UNC5C.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.6 |
14
-|DLBCL |Schmitz cohort|5.1 |
15
-|DLBCL |Reddy cohort |2.2 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.44 |
13
+|DLBCL |Schmitz cohort|5.10 |
14
+|DLBCL |Reddy cohort |2.20 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.406 |0 |
23 22
|DLBCL |No |No |1.948 |0 |
24 23
|FL |No |No |1.266 |0 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5C_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/UNC5C_NM_003728.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5C.html)
32
+
33
+![image](../../images/proteinpaint/UNC5C.svg)
UNC5D.md
... ...
@@ -2,15 +2,14 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
14 13
|DLBCL |Schmitz cohort|1.9 |
15 14
|DLBCL |Reddy cohort |1.8 |
16 15
|DLBCL |Chapuy cohort |2.6 |
... ...
@@ -18,8 +17,17 @@
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.954 |5.751 |
23 22
|DLBCL |No |No |1.655 |2.419 |
24 23
|FL |No |No |1.545 |0.000 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5D_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/UNC5D_NM_080872.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5D.html)
32
+
33
+![image](../../images/proteinpaint/UNC5D.svg)
USP7.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |1 |high-confidence DLBCL gene|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|6.47 |
15 14
|BL |Thomas cohort |6.80 |
16 15
|BL |Panea cohort |5.90 |
17
-|DLBCL |GAMBL genomes |1.60 |
16
+|DLBCL |GAMBL genomes |1.34 |
18 17
|DLBCL |Schmitz cohort |3.20 |
19 18
|DLBCL |Reddy cohort |1.10 |
20 19
|DLBCL |Chapuy cohort |3.80 |
... ...
@@ -22,8 +21,17 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |Yes |3.462 |21.705 |
27 26
|DLBCL |No |No |0.938 | 0.000 |
28 27
|FL |No |No |0.000 |15.446 |
29 28
29
+
30
+
31
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/USP7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/USP7_protein_hg38.html)
32
+
33
+![image](../../images/proteinpaint/USP7_NM_003470.svg)
34
+
35
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/USP7.html)
36
+
37
+![image](../../images/proteinpaint/USP7.svg)
VMA21.md
... ...
@@ -2,21 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------|
7
+|FL |1 |high-confidence FL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|5.08 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No | 0.000 | 0.000 |
20 19
|DLBCL |No |No | 3.430 | 81.281 |
21 20
|FL |No |Yes |25.632 |598.612 |
22 21
22
+
23
+> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VMA21_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VMA21_protein_hg38.html)
27
+
28
+![image](../../images/proteinpaint/VMA21_NM_001017980.svg)
29
+
30
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VMA21.html)
31
+
32
+![image](../../images/proteinpaint/VMA21.svg)
VPS13B.md
... ...
@@ -2,24 +2,32 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |4.1 |
14
-|DLBCL |Schmitz cohort|8.3 |
15
-|DLBCL |Reddy cohort |5.7 |
16
-|DLBCL |Chapuy cohort |4.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.21 |
13
+|DLBCL |Schmitz cohort|8.30 |
14
+|DLBCL |Reddy cohort |5.70 |
15
+|DLBCL |Chapuy cohort |4.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.768 |0.000 |
23 22
|DLBCL |No |No |1.730 |0.000 |
24 23
|FL |No |No |0.000 |4.014 |
25 24
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VPS13B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VPS13B_protein_hg38.html)
28
+
29
+![image](../../images/proteinpaint/VPS13B_NM_152564.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VPS13B.html)
32
+
33
+![image](../../images/proteinpaint/VPS13B.svg)
VWA7.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.954 |0 |
22 21
|DLBCL |No |No |1.059 |0 |
23 22
|FL |No |No |1.950 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VWA7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VWA7_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/VWA7_NM_025258.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VWA7.html)
7
+
8
+![image](../../images/proteinpaint/VWA7.svg)
WAC.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.8 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |1.2 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.68 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.957 |0 |
23 22
|DLBCL |No |No |1.590 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WAC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WAC_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/WAC_NM_016628.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WAC.html)
7
+
8
+![image](../../images/proteinpaint/WAC.svg)
WDR7.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|2.08 |
14 13
|BL |Thomas cohort |0.40 |
15 14
|BL |Panea cohort |6.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.257 |0.000 |
22 21
|DLBCL |No |No |0.454 |0.000 |
23 22
|FL |No |No |1.904 |8.746 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDR7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDR7_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/WDR7_NM_015285.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDR7.html)
7
+
8
+![image](../../images/proteinpaint/WDR7.svg)
WDR90.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.62 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.227 |0 |
22 21
|DLBCL |No |No |1.118 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDR90_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDR90_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/WDR90_NM_145294.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDR90.html)
7
+
8
+![image](../../images/proteinpaint/WDR90.svg)
WEE1.md
... ...
@@ -2,29 +2,37 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.8 |
14
-|DLBCL |Schmitz cohort|2.8 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort |1.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.02 |
13
+|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |1.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |4.336 | 0.000 |
23 22
|DLBCL |Yes |Yes |8.073 |15.059 |
24 23
|FL |Yes |No |4.041 | 0.000 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr11 |9595246 |9599502 |intron|NA |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr11 |9595246 |9599502 |[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A9595246%2D9599502)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WEE1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WEE1_protein_hg38.html)
33
+
34
+![image](../../images/proteinpaint/WEE1_NM_003390.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WEE1.html)
37
+
38
+![image](../../images/proteinpaint/WEE1.svg)
WHAMM.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.15 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.909 | 0.000 |
22 21
|DLBCL |No |No |0.000 |12.559 |
23 22
|FL |No |No |0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WHAMM_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WHAMM_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/WHAMM_NM_001080435.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WHAMM.html)
7
+
8
+![image](../../images/proteinpaint/WHAMM.svg)
WNK1.md
... ...
@@ -2,26 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |1 |high-confidence BL gene |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 9
## Mutation incidence
10 10
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
13
-|BL |GAMBL genomes+capture| 6.7 |
14
-|BL |Thomas cohort | 6.8 |
15
-|BL |Panea cohort |11.9 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture| 6.70 |
14
+|BL |Thomas cohort | 6.80 |
15
+|BL |Panea cohort |11.90 |
16
+|DLBCL |GAMBL genomes | 4.59 |
17
+|DLBCL |Schmitz cohort | NA |
18
+|DLBCL |Reddy cohort | NA |
19
+|DLBCL |Chapuy cohort | NA |
16 20
17 21
## Mutation pattern
18 22
19 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 25
|BL |No |No |3.429 |0 |
22 26
|DLBCL |No |No |1.812 |0 |
23 27
|FL |No |No |3.487 |0 |
24 28
25 29
26 30
> [!NOTE]
27
-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743)
... ...
\ No newline at end of file
0
+> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WNK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WNK1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/WNK1_NM_018979.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WNK1.html)
7
+
8
+![image](../../images/proteinpaint/WNK1.svg)
WNK2.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture| 3.23 |
14 13
|BL |Thomas cohort | 0.80 |
15 14
|BL |Panea cohort |10.90 |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.309 |0 |
22 21
|DLBCL |No |No |0.637 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
... ...
\ No newline at end of file
0
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WNK2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WNK2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/WNK2_NM_006648.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WNK2.html)
7
+
8
+![image](../../images/proteinpaint/WNK2.svg)
XBP1.md
... ...
@@ -2,29 +2,37 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|1.3 |
15
-|DLBCL |Reddy cohort |1.6 |
16
-|DLBCL |Chapuy cohort | NA |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|1.30 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort | NA |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |Yes |No |1.624 |39.881 |
23 22
|DLBCL |Yes |No |1.835 | 0.000 |
24 23
|FL |Yes |No |2.607 | 0.000 |
25 24
26 25
## aSHM regions
27 26
28
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
29
-|--------|----------|--------|------|------------------|
30
-|chr22 |29194943 |29197461|TSS |NA |
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr22 |29194943 |29197461|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr22%3A29194943%2D29197461)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XBP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XBP1_protein_hg38.html)
33
+
34
+![image](../../images/proteinpaint/XBP1_NM_005080.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XBP1.html)
37
+
38
+![image](../../images/proteinpaint/XBP1.svg)
XIRP2.md
... ...
@@ -2,24 +2,31 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|FL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|FL |2 |relevance in FL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|-------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
13 12
|FL |GAMBL genomes|3.93 |
14 13
15 14
## Mutation pattern
16 15
17 16
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
18
-|------|----|---------------------|----------------|----------------|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19 18
|BL |No |No |0.000 |0.000 |
20 19
|DLBCL |No |No |2.268 |2.044 |
21 20
|FL |No |No |0.000 |0.000 |
22 21
23 22
24 23
> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
... ...
\ No newline at end of file
0
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XIRP2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XIRP2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/XIRP2_NM_152381.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XIRP2.html)
7
+
8
+![image](../../images/proteinpaint/XIRP2.svg)
XPO1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.2 |
14
-|DLBCL |Schmitz cohort|2.3 |
15
-|DLBCL |Reddy cohort |1.4 |
16
-|DLBCL |Chapuy cohort |1.3 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|2.30 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |1.30 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.028 |0 |
23 22
|DLBCL |No |No |9.927 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2016 by [Mareschal S](https://pubmed.ncbi.nlm.nih.gov/26608593)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2016 by [Mareschal S](https://pubmed.ncbi.nlm.nih.gov/26608593)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XPO1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XPO1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/XPO1_NM_003400.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XPO1.html)
7
+
8
+![image](../../images/proteinpaint/XPO1.svg)
YY1.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.1 |
14
-|DLBCL |Schmitz cohort|4.3 |
15
-|DLBCL |Reddy cohort |1.1 |
16
-|DLBCL |Chapuy cohort |3.8 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|4.30 |
14
+|DLBCL |Reddy cohort |1.10 |
15
+|DLBCL |Chapuy cohort |3.80 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |6.553 | 0.000 |
23 22
|DLBCL |No |No |3.473 |57.733 |
24 23
|FL |No |No |3.554 |61.850 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/YY1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/YY1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/YY1_NM_003403.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/YY1.html)
7
+
8
+![image](../../images/proteinpaint/YY1.svg)
YY1AP1.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|1.85 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |1.988 |14.209 |
22 21
|DLBCL |No |No |0.000 | 0.000 |
23 22
|FL |No |No |0.000 | 0.000 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/YY1AP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/YY1AP1_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/YY1AP1_NM_139118.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/YY1AP1.html)
7
+
8
+![image](../../images/proteinpaint/YY1AP1.svg)
ZAN.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|5.77 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,8 +16,16 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
22 21
23 22
> [!NOTE]
24
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZAN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZAN_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZAN_NM_003386.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZAN.html)
7
+
8
+![image](../../images/proteinpaint/ZAN.svg)
ZBTB7A.md
... ...
@@ -2,31 +2,38 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
14
-|BL |GAMBL genomes+capture|3.0 |
15
-|BL |Thomas cohort | NA |
16
-|BL |Panea cohort | NA |
17
-|DLBCL |GAMBL genomes |1.8 |
18
-|DLBCL |Schmitz cohort |1.5 |
19
-|DLBCL |Reddy cohort |1.3 |
20
-|DLBCL |Chapuy cohort |1.7 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture|3.00 |
14
+|BL |Thomas cohort | NA |
15
+|BL |Panea cohort | NA |
16
+|DLBCL |GAMBL genomes |1.72 |
17
+|DLBCL |Schmitz cohort |1.50 |
18
+|DLBCL |Reddy cohort |1.30 |
19
+|DLBCL |Chapuy cohort |1.70 |
21 20
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |No |No |4.693 |0 |
27 26
|DLBCL |No |No |1.625 |0 |
28 27
|FL |No |No |0.000 |0 |
29 28
30 29
31 30
> [!NOTE]
32
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZBTB7A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZBTB7A_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZBTB7A_NM_015898.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZBTB7A.html)
7
+
8
+![image](../../images/proteinpaint/ZBTB7A.svg)
ZC3H12A.md
... ...
@@ -2,16 +2,15 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-|FL |2 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene |
8
+|FL |2 |relevance in FL not firmly established|
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|--------------|-------------|
14
-|DLBCL |GAMBL genomes |3.20 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |2.68 |
15 14
|DLBCL |Schmitz cohort|6.00 |
16 15
|DLBCL |Reddy cohort |3.10 |
17 16
|DLBCL |Chapuy cohort |4.70 |
... ...
@@ -20,8 +19,17 @@
20 19
## Mutation pattern
21 20
22 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23
-|------|----|---------------------|----------------|----------------|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
24 23
|BL |No |No |0.000 | 0.000 |
25 24
|DLBCL |No |No |2.488 |18.944 |
26 25
|FL |No |No |0.000 | 0.000 |
27 26
27
+
28
+
29
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZC3H12A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZC3H12A_protein_hg38.html)
30
+
31
+![image](../../images/proteinpaint/ZC3H12A_NM_025079.svg)
32
+
33
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZC3H12A.html)
34
+
35
+![image](../../images/proteinpaint/ZC3H12A.svg)
ZEB2.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |3.4 |
14
-|DLBCL |Schmitz cohort|6.8 |
15
-|DLBCL |Reddy cohort |3.7 |
16
-|DLBCL |Chapuy cohort |6.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.82 |
13
+|DLBCL |Schmitz cohort|6.80 |
14
+|DLBCL |Reddy cohort |3.70 |
15
+|DLBCL |Chapuy cohort |6.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 | 0.000 |
23 22
|DLBCL |No |Yes |1.406 |33.261 |
24 23
|FL |No |No |2.638 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZEB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZEB2_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZEB2_NM_014795.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZEB2.html)
7
+
8
+![image](../../images/proteinpaint/ZEB2.svg)
ZFAT.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.9 |
14
-|DLBCL |Schmitz cohort|2.8 |
15
-|DLBCL |Reddy cohort |2.7 |
16
-|DLBCL |Chapuy cohort |2.6 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Reddy cohort |2.70 |
15
+|DLBCL |Chapuy cohort |2.60 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.000 |0 |
23 22
|DLBCL |No |No |1.873 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFAT_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFAT_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZFAT_NM_020863.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFAT.html)
7
+
8
+![image](../../images/proteinpaint/ZFAT.svg)
ZFP36L1.md
... ...
@@ -2,19 +2,18 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-|DLBCL |1 |
9
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12
-|Entity|study |frequency (%)|
13
-|------|---------------------|-------------|
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
14 13
|BL |GAMBL genomes+capture|2.08 |
15 14
|BL |Thomas cohort |2.10 |
16 15
|BL |Panea cohort |3.00 |
17
-|DLBCL |GAMBL genomes |5.60 |
16
+|DLBCL |GAMBL genomes |6.69 |
18 17
|DLBCL |Schmitz cohort |8.50 |
19 18
|DLBCL |Reddy cohort |5.60 |
20 19
|DLBCL |Chapuy cohort |8.10 |
... ...
@@ -22,13 +21,22 @@
22 21
## Mutation pattern
23 22
24 23
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25
-|------|----|---------------------|----------------|----------------|
24
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
26 25
|BL |Yes |Yes |2.453 |185.809 |
27 26
|DLBCL |Yes |Yes |1.293 | 14.964 |
28 27
|FL |Yes |Yes |7.622 |419.109 |
29 28
30 29
## aSHM regions
31 30
32
-|chr_name|hg19_start|hg19_end|region|regulatory_comment|
33
-|--------|----------|--------|------|------------------|
34
-|chr14 |69257848 |69259739|TSS |active_promoter |
31
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
32
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
33
+|chr14 |69257848 |69259739|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr14%3A69257848%2D69259739)|active_promoter |
34
+
35
+
36
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFP36L1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFP36L1_protein_hg38.html)
37
+
38
+![image](../../images/proteinpaint/ZFP36L1_NM_004926.svg)
39
+
40
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFP36L1.html)
41
+
42
+![image](../../images/proteinpaint/ZFP36L1.svg)
ZFX.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |0.5 |
14
-|DLBCL |Schmitz cohort|1.7 |
15
-|DLBCL |Reddy cohort |1.4 |
16
-|DLBCL |Chapuy cohort |0.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|1.70 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |0.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |3.677 |0 |
23 22
|DLBCL |No |No |0.000 |0 |
24 23
|FL |No |No |0.000 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFX_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFX_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZFX_NM_003410.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFX.html)
7
+
8
+![image](../../images/proteinpaint/ZFX.svg)
ZNF217.md
... ...
@@ -0,0 +1,27 @@
1
+# [ZNF217]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.1 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.310 |0 |
22
+|DLBCL |No |No |2.456 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
ZNF229.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.69 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.954 |0 |
22 21
|DLBCL |No |No |1.346 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
... ...
\ No newline at end of file
0
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF229_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF229_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZNF229_NM_014518.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF229.html)
7
+
8
+![image](../../images/proteinpaint/ZNF229.svg)
ZNF292.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |1 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |5.2 |
14
-|DLBCL |Schmitz cohort|6.4 |
15
-|DLBCL |Reddy cohort |4.3 |
16
-|DLBCL |Chapuy cohort |6.0 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |5.35 |
13
+|DLBCL |Schmitz cohort|6.40 |
14
+|DLBCL |Reddy cohort |4.30 |
15
+|DLBCL |Chapuy cohort |6.00 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |1.036 | 2.462 |
23 22
|DLBCL |No |No |1.272 |11.022 |
24 23
|FL |No |No |2.049 | 0.000 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF292_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF292_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZNF292_NM_015021.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF292.html)
7
+
8
+![image](../../images/proteinpaint/ZNF292.svg)
ZNF423.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |1.8 |
14
-|DLBCL |Schmitz cohort|3.4 |
15
-|DLBCL |Reddy cohort |2.1 |
16
-|DLBCL |Chapuy cohort |3.4 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |3.40 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.594 |0 |
23 22
|DLBCL |No |No |1.430 |0 |
24 23
|FL |No |No |0.836 |0 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF423_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF423_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZNF423_NM_015069.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF423.html)
7
+
8
+![image](../../images/proteinpaint/ZNF423.svg)
ZNF608.md
... ...
@@ -2,27 +2,34 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|DLBCL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------|
7
+|DLBCL |1 |high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|--------------|-------------|
13
-|DLBCL |GAMBL genomes |6.3 |
14
-|DLBCL |Schmitz cohort|9.4 |
15
-|DLBCL |Reddy cohort |8.1 |
16
-|DLBCL |Chapuy cohort |7.7 |
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |6.12 |
13
+|DLBCL |Schmitz cohort|9.40 |
14
+|DLBCL |Reddy cohort |8.10 |
15
+|DLBCL |Chapuy cohort |7.70 |
17 16
18 17
## Mutation pattern
19 18
20 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21
-|------|----|---------------------|----------------|----------------|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
22 21
|BL |No |No |0.986 |0.000 |
23 22
|DLBCL |No |No |1.714 |3.638 |
24 23
|FL |No |No |1.867 |4.218 |
25 24
26 25
27 26
> [!NOTE]
28
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF608_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF608_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZNF608_NM_020747.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF608.html)
7
+
8
+![image](../../images/proteinpaint/ZNF608.svg)
ZNF85.md
... ...
@@ -2,14 +2,13 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|
6
-|------|----|
7
-|BL |2 |
8
-
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
9 8
## Mutation incidence
10 9
11
-|Entity|study |frequency (%)|
12
-|------|---------------------|-------------|
10
+|Entity|source |frequency (%)|
11
+|:------:|:---------------------:|:-------------:|
13 12
|BL |GAMBL genomes+capture|0.69 |
14 13
|BL |Thomas cohort | NA |
15 14
|BL |Panea cohort | NA |
... ...
@@ -17,11 +16,19 @@
17 16
## Mutation pattern
18 17
19 18
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|------|----|---------------------|----------------|----------------|
19
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21 20
|BL |No |No |0.000 |0 |
22 21
|DLBCL |No |No |1.446 |0 |
23 22
|FL |No |No |0.000 |0 |
24 23
25 24
26 25
> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
... ...
\ No newline at end of file
0
+> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
1
+
2
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF85_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF85_protein_hg38.html)
3
+
4
+![image](../../images/proteinpaint/ZNF85_NM_003429.svg)
5
+
6
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF85.html)
7
+
8
+![image](../../images/proteinpaint/ZNF85.svg)