IRF4.md
... ...
@@ -1,12 +1,15 @@
1
+# IRF4
2
+## Overview
1 3
IRF4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 10
|FL |1-a | aSHM target and high-confidence FL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +19,7 @@ IRF4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 19
|DLBCL |Chapuy cohort |2.14 |
17 20
|FL |GAMBL genomes |1.15 |
18 21
19
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
20 23
21 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
IRF8.md
... ...
@@ -1,13 +1,16 @@
1
+# IRF8
2
+## Overview
1 3
IRF8 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ IRF8 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
20 23
|DLBCL |Chapuy cohort |10.26 |
21 24
|FL |GAMBL genomes |12.01 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ITPKB.md
... ...
@@ -1,12 +1,15 @@
1
+# ITPKB
2
+## Overview
1 3
ITPKB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 10
|FL |1-a | aSHM target and high-confidence FL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +19,7 @@ ITPKB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 19
|DLBCL |Chapuy cohort |9.40 |
17 20
|FL |GAMBL genomes |3.23 |
18 21
19
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
20 23
21 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ITPR3.md
... ...
@@ -1,11 +1,12 @@
1
-# [ITPR3]
1
+# ITPR3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
JAK1.md
... ...
@@ -1,11 +1,12 @@
1
-# [JAK1]
1
+# JAK1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.20 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
JAK3.md
... ...
@@ -1,11 +1,12 @@
1
-# [JAK3]
1
+# JAK3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.00 |
15 16
|DLBCL |Chapuy cohort | NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
JUNB.md
... ...
@@ -1,11 +1,12 @@
1
-# [JUNB]
1
+# JUNB
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |3.50 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
JUP.md
... ...
@@ -1,17 +1,18 @@
1
-# [JUP]
1
+# JUP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.15 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KCMF1.md
... ...
@@ -1,11 +1,12 @@
1
-# [KCMF1]
1
+# KCMF1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.00 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KCNK10.md
... ...
@@ -1,11 +1,12 @@
1
-# [KCNK10]
1
+# KCNK10
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |0.80 |
14 15
|BL |Panea cohort |1.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KIFC3.md
... ...
@@ -1,11 +1,12 @@
1
-# [KIFC3]
1
+# KIFC3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KIR3DL1.md
... ...
@@ -1,17 +1,18 @@
1
-# [KIR3DL1]
1
+# KIR3DL1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.15 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KLF2.md
... ...
@@ -1,12 +1,15 @@
1
+# KLF2
2
+## Overview
1 3
KLF2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 10
|FL |1-a | aSHM target and high-confidence FL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +19,7 @@ KLF2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 19
|DLBCL |Chapuy cohort |2.99 |
17 20
|FL |GAMBL genomes |2.31 |
18 21
19
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
20 23
21 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KLHL14.md
... ...
@@ -1,11 +1,12 @@
1
-# [KLHL14]
1
+# KLHL14
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.60 |
15 16
|DLBCL |Chapuy cohort |7.26 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KLHL21.md
... ...
@@ -1,11 +1,12 @@
1
-# [KLHL21]
1
+# KLHL21
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.50 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KLHL26.md
... ...
@@ -1,11 +1,12 @@
1
-# [KLHL26]
1
+# KLHL26
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KLHL6.md
... ...
@@ -1,13 +1,16 @@
1
+# KLHL6
2
+##Overview
1 3
KLHL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ KLHL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
20 23
|DLBCL |Chapuy cohort |8.97 |
21 24
|FL |GAMBL genomes |7.16 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KMT2C.md
... ...
@@ -1,13 +1,14 @@
1
-# [KMT2C]
1
+# KMT2C
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established |
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|MCL |2 |relevance in MCL not firmly established|
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort |6.41 |
21 22
|MCL |GAMBL genomes |0.47 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KMT2D.md
... ...
@@ -1,6 +1,6 @@
1
-# [KMT2D]
1
+# KMT2D
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
... ...
@@ -8,7 +8,8 @@
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9 9
|FL |1 |high-confidence FL gene |
10 10
|MCL |1 |high-confidence MCL gene |
11
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 13
13 14
|Entity|source |frequency (%)|
14 15
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +23,7 @@
22 23
|FL |GAMBL genomes |67.67 |
23 24
|MCL |GAMBL genomes |16.59 |
24 25
25
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
26 27
27 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
KRAS.md
... ...
@@ -1,11 +1,12 @@
1
-# [KRAS]
1
+# KRAS
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.70 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LAMA5.md
... ...
@@ -1,11 +1,12 @@
1
-# [LAMA5]
1
+# LAMA5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | 4.70 |
15 16
|DLBCL |Chapuy cohort | 5.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LAPTM5.md
... ...
@@ -1,12 +1,13 @@
1
-# [LAPTM5]
1
+# LAPTM5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |2.56 |
17 18
|FL |GAMBL genomes |5.77 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LCOR.md
... ...
@@ -1,12 +1,13 @@
1
-# [LCOR]
1
+# LCOR
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |0.50 |
19 20
|DLBCL |Chapuy cohort |0.43 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LIN54.md
... ...
@@ -1,11 +1,12 @@
1
-# [LIN54]
1
+# LIN54
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.90 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LPP.md
... ...
@@ -1,11 +1,12 @@
1
-# [LPP]
1
+# LPP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LRP12.md
... ...
@@ -1,11 +1,12 @@
1
-# [LRP12]
1
+# LRP12
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.40 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LRRN3.md
... ...
@@ -1,11 +1,12 @@
1
-# [LRRN3]
1
+# LRRN3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |6.51 |
15 16
|DLBCL |Chapuy cohort |6.84 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LTB.md
... ...
@@ -1,13 +1,16 @@
1
+# LTB
2
+## Overview
1 3
LTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ LTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
20 23
|DLBCL |Chapuy cohort |9.83 |
21 24
|FL |GAMBL genomes |8.78 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
LYN.md
... ...
@@ -1,11 +1,12 @@
1
-# [LYN]
1
+# LYN
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |5.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MAGEC1.md
... ...
@@ -1,17 +1,18 @@
1
-# [MAGEC1]
1
+# MAGEC1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.85 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MAGT1.md
... ...
@@ -1,11 +1,12 @@
1
-# [MAGT1]
1
+# MAGT1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.90 |
15 16
|DLBCL |Chapuy cohort |1.71 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MALAT1.md
... ...
@@ -1,11 +1,12 @@
1
-# [MALAT1]
1
+# MALAT1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
MAP2K1.md
... ...
@@ -1,12 +1,13 @@
1
-# [MAP2K1]
1
+# MAP2K1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8 8
|FL |1 |high-confidence FL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |2.14 |
17 18
|FL |GAMBL genomes |1.39 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MAP3K6.md
... ...
@@ -1,11 +1,12 @@
1
-# [MAP3K6]
1
+# MAP3K6
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MAP4K4.md
... ...
@@ -1,11 +1,12 @@
1
-# [MAP4K4]
1
+# MAP4K4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.10 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MAP7D1.md
... ...
@@ -1,17 +1,18 @@
1
-# [MAP7D1]
1
+# MAP7D1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|NA |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MARK1.md
... ...
@@ -1,11 +1,12 @@
1
-# [MARK1]
1
+# MARK1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MCL1.md
... ...
@@ -1,12 +1,15 @@
1
+# MCL1
2
+## Overview
1 3
MCL1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +21,7 @@ MCL1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
18 21
|DLBCL |Reddy cohort |4.70 |
19 22
|DLBCL |Chapuy cohort |3.42 |
20 23
21
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
22 25
23 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MECOM.md
... ...
@@ -1,11 +1,12 @@
1
-# [MECOM]
1
+# MECOM
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.10 |
15 16
|DLBCL |Chapuy cohort |3.42 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MEF2B.md
... ...
@@ -1,6 +1,8 @@
1
+# MEF2B
2
+## Overview
1 3
MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. MEF2B mutations are observed in a significant subset of follicular lymphoma cases, as well as in other B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL). MEF2B has known hotspot mutations that affect multiple distinct domains of the protein.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
... ...
@@ -8,7 +10,8 @@ MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |1-a | aSHM target and high-confidence FL gene |
10 12
11
-## Mutation incidence
13
+
14
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 15
13 16
|Entity|source |frequency (%)|
14 17
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +25,7 @@ MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
22 25
|FL |GAMBL genomes |12.93 |
23 26
|MCL |GAMBL genomes | 5.69 |
24 27
25
-## Mutation pattern
28
+## Mutation pattern and selective pressure estimates
26 29
27 30
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 31
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MEF2C.md
... ...
@@ -1,12 +1,15 @@
1
+# MEF2C
2
+## Overview
1 3
MEF2C is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 10
|FL |1-a | aSHM target and high-confidence FL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +19,7 @@ MEF2C is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 19
|DLBCL |Chapuy cohort |2.99 |
17 20
|FL |GAMBL genomes |6.24 |
18 21
19
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
20 23
21 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MET.md
... ...
@@ -1,11 +1,12 @@
1
-# [MET]
1
+# MET
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.70 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MGA.md
... ...
@@ -1,11 +1,12 @@
1
-# [MGA]
1
+# MGA
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.70 |
15 16
|DLBCL |Chapuy cohort |3.42 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MGEA5.md
... ...
@@ -1,17 +1,18 @@
1
-# [MGEA5]
1
+# MGEA5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.85 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MIR142.md
... ...
@@ -1,12 +1,13 @@
1
-# [MIR142]
1
+# MIR142
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established |
8 8
|DLBCL |2 |relevance in DLBCL not firmly established|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |NA |
19 20
|DLBCL |Chapuy cohort |NA |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|
24 25
MIR155HG.md
... ...
@@ -1,11 +1,12 @@
1
-# [MIR155HG]
1
+# MIR155HG
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | NA |
15 16
|DLBCL |Chapuy cohort | NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
MKI67.md
... ...
@@ -1,12 +1,13 @@
1
-# [MKI67]
1
+# MKI67
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|FL |2 |relevance in FL not firmly established|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -15,7 +16,7 @@
15 16
|BL |Panea cohort | NA |
16 17
|FL |GAMBL genomes |1.15 |
17 18
18
-## Mutation pattern
19
+## Mutation pattern and selective pressure estimates
19 20
20 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21 22
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MME.md
... ...
@@ -1,11 +1,12 @@
1
-# [MME]
1
+# MME
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |0.80 |
14 15
|BL |Panea cohort |5.90 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MPDZ.md
... ...
@@ -1,11 +1,12 @@
1
-# [MPDZ]
1
+# MPDZ
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | 5.61 |
15 16
|DLBCL |Chapuy cohort | 2.99 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MPEG1.md
... ...
@@ -1,11 +1,12 @@
1
-# [MPEG1]
1
+# MPEG1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | 5.81 |
15 16
|DLBCL |Chapuy cohort |10.68 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MRGPRF.md
... ...
@@ -1,17 +1,18 @@
1
-# [MRGPRF]
1
+# MRGPRF
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|0 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MS4A1.md
... ...
@@ -1,11 +1,14 @@
1
+# MS4A1
2
+## Overview
1 3
MS4A1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 12
10 13
|Entity|source |frequency (%)|
11 14
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +17,7 @@ MS4A1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
14 17
|DLBCL |Reddy cohort |1.30 |
15 18
|DLBCL |Chapuy cohort |0.43 |
16 19
17
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
18 21
19 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MSH2.md
... ...
@@ -1,11 +1,12 @@
1
-# [MSH2]
1
+# MSH2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.50 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MSH6.md
... ...
@@ -1,11 +1,12 @@
1
-# [MSH6]
1
+# MSH6
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.60 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MTOR.md
... ...
@@ -1,12 +1,13 @@
1
-# [MTOR]
1
+# MTOR
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort | 2.40 |
19 20
|DLBCL |Chapuy cohort | 2.14 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYB.md
... ...
@@ -1,11 +1,12 @@
1
-# [MYB]
1
+# MYB
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.10 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYBPC2.md
... ...
@@ -1,11 +1,12 @@
1
-# [MYBPC2]
1
+# MYBPC2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.80 |
15 16
|DLBCL |Chapuy cohort |1.71 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYC.md
... ...
@@ -1,13 +1,16 @@
1
+# MYC
2
+## Overview
1 3
MYC is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |1-a | aSHM target and high-confidence BL gene |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ MYC is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
20 23
|DLBCL |Chapuy cohort | 6.41 |
21 24
|FL |GAMBL genomes | 0.92 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYCBP2.md
... ...
@@ -1,17 +1,18 @@
1
-# [MYCBP2]
1
+# MYCBP2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|3 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYD88.md
... ...
@@ -1,13 +1,14 @@
1
-# [MYD88]
1
+# MYD88
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|FL |2 |relevance in FL not firmly established|
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort |21.37 |
21 22
|FL |GAMBL genomes | 1.85 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYH10.md
... ...
@@ -1,11 +1,12 @@
1
-# [MYH10]
1
+# MYH10
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYO18A.md
... ...
@@ -1,11 +1,12 @@
1
-# [MYO18A]
1
+# MYO18A
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYO1E.md
... ...
@@ -1,12 +1,13 @@
1
-# [MYO1E]
1
+# MYO1E
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |3.00 |
19 20
|DLBCL |Chapuy cohort |1.28 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
MYOM2.md
... ...
@@ -1,11 +1,12 @@
1
-# [MYOM2]
1
+# MYOM2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |3.20 |
15 16
|DLBCL |Chapuy cohort |4.27 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
N2RF2.md
... ...
@@ -1,11 +1,12 @@
1
-# [N2RF2]
1
+# N2RF2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
NANOG.md
... ...
@@ -1,11 +1,12 @@
1
-# [NANOG]
1
+# NANOG
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.40 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NAV1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NAV1]
1
+# NAV1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.00 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NBEAL1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NBEAL1]
1
+# NBEAL1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NCOA3.md
... ...
@@ -1,11 +1,12 @@
1
-# [NCOA3]
1
+# NCOA3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.40 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NCOR1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NCOR1]
1
+# NCOR1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.70 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NCOR2.md
... ...
@@ -1,12 +1,13 @@
1
-# [NCOR2]
1
+# NCOR2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |3.60 |
19 20
|DLBCL |Chapuy cohort |4.27 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NEAT1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NEAT1]
1
+# NEAT1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
NF1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NF1]
1
+# NF1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.50 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NFKB1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NFKB1]
1
+# NFKB1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.60 |
15 16
|DLBCL |Chapuy cohort |3.42 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NFKB2.md
... ...
@@ -1,11 +1,12 @@
1
-# [NFKB2]
1
+# NFKB2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.40 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NFKBIA.md
... ...
@@ -1,13 +1,14 @@
1
-# [NFKBIA]
1
+# NFKBIA
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|FL |2 |relevance in FL not firmly established|
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort |4.70 |
21 22
|FL |GAMBL genomes |0.69 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NFKBIE.md
... ...
@@ -1,12 +1,13 @@
1
-# [NFKBIE]
1
+# NFKBIE
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|MCL |1 |high-confidence MCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |3.42 |
17 18
|MCL |GAMBL genomes |2.84 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NFKBIZ.md
... ...
@@ -1,11 +1,14 @@
1
+# NFKBIZ
2
+## Overview
1 3
NFKBIZ is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 12
10 13
|Entity|source |frequency (%)|
11 14
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +17,7 @@ NFKBIZ is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
14 17
|DLBCL |Reddy cohort |1.50 |
15 18
|DLBCL |Chapuy cohort |0.85 |
16 19
17
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
18 21
19 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NFKBIZ.pdf
... ...
Binary files /dev/null and b/NFKBIZ.pdf differ
NIN.md
... ...
@@ -1,17 +1,18 @@
1
-# [NIN]
1
+# NIN
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|0 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NLRC5.md
... ...
@@ -1,11 +1,12 @@
1
-# [NLRC5]
1
+# NLRC5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |3.70 |
15 16
|DLBCL |Chapuy cohort |2.99 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NLRP5.md
... ...
@@ -1,11 +1,12 @@
1
-# [NLRP5]
1
+# NLRP5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.20 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NLRP8.md
... ...
@@ -1,11 +1,12 @@
1
-# [NLRP8]
1
+# NLRP8
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.10 |
15 16
|DLBCL |Chapuy cohort |3.42 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NOA1.md
... ...
@@ -1,11 +1,12 @@
1
-# [NOA1]
1
+# NOA1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NOL9.md
... ...
@@ -1,11 +1,12 @@
1
-# [NOL9]
1
+# NOL9
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NOTCH1.md
... ...
@@ -1,13 +1,14 @@
1
-# [NOTCH1]
1
+# NOTCH1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|MCL |1 |high-confidence MCL gene |
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort |2.99 |
21 22
|MCL |GAMBL genomes |5.21 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NOTCH2.md
... ...
@@ -1,13 +1,14 @@
1
-# [NOTCH2]
1
+# NOTCH2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|MCL |1 |high-confidence MCL gene |
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort | 7.26 |
21 22
|MCL |GAMBL genomes | 2.84 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NRXN2.md
... ...
@@ -1,11 +1,12 @@
1
-# [NRXN2]
1
+# NRXN2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
NSD2.md
... ...
@@ -1,17 +1,18 @@
1
-# [NSD2]
1
+# NSD2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7 7
|MCL |1 |high-confidence MCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|7.11 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|
17 18
ODZ3.md
... ...
@@ -1,11 +1,12 @@
1
-# [ODZ3]
1
+# ODZ3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
OGDHL.md
... ...
@@ -1,17 +1,18 @@
1
-# [OGDHL]
1
+# OGDHL
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|1.42 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
OR8H2.md
... ...
@@ -1,17 +1,18 @@
1
-# [OR8H2]
1
+# OR8H2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.15 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
OSBPL10.md
... ...
@@ -1,12 +1,15 @@
1
+# OSBPL10
2
+## Overview
1 3
OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +21,7 @@ OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
18 21
|DLBCL |Reddy cohort | 2.30 |
19 22
|DLBCL |Chapuy cohort | 2.56 |
20 23
21
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
22 25
23 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
P2RX5.md
... ...
@@ -1,11 +1,12 @@
1
-# [P2RX5]
1
+# P2RX5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.60 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
P2RY2.md
... ...
@@ -1,11 +1,12 @@
1
-# [P2RY2]
1
+# P2RY2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
P2RY8.md
... ...
@@ -1,13 +1,14 @@
1
-# [P2RY8]
1
+# P2RY8
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|FL |2 |relevance in FL not firmly established|
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort | 5.98 |
21 22
|FL |GAMBL genomes | 2.31 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PABPC4L.md
... ...
@@ -1,11 +1,12 @@
1
-# [PABPC4L]
1
+# PABPC4L
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |1.30 |
14 15
|BL |Panea cohort |3.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PAPOLG.md
... ...
@@ -1,11 +1,12 @@
1
-# [PAPOLG]
1
+# PAPOLG
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.20 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PASK.md
... ...
@@ -1,11 +1,12 @@
1
-# [PASK]
1
+# PASK
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.00 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PAX5.md
... ...
@@ -1,11 +1,12 @@
1
-# [PAX5]
1
+# PAX5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.90 |
15 16
|DLBCL |Chapuy cohort |3.42 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PC.md
... ...
@@ -1,11 +1,12 @@
1
-# [PC]
1
+# PC
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PDE4DIP.md
... ...
@@ -1,11 +1,12 @@
1
-# [PDE4DIP]
1
+# PDE4DIP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |5.31 |
15 16
|DLBCL |Chapuy cohort |8.55 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PKD1.md
... ...
@@ -1,11 +1,12 @@
1
-# [PKD1]
1
+# PKD1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.70 |
15 16
|DLBCL |Chapuy cohort |6.41 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PLCG2.md
... ...
@@ -1,11 +1,12 @@
1
-# [PLCG2]
1
+# PLCG2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | 0.8 |
14 15
|BL |Panea cohort |10.9 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PLXNB3.md
... ...
@@ -1,17 +1,18 @@
1
-# [PLXNB3]
1
+# PLXNB3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|0 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PMAIP1.md
... ...
@@ -1,11 +1,12 @@
1
-# [PMAIP1]
1
+# PMAIP1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |3.00 |
14 15
|BL |Panea cohort |5.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PNPO.md
... ...
@@ -1,11 +1,12 @@
1
-# [PNPO]
1
+# PNPO
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.30 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
POGZ.md
... ...
@@ -1,11 +1,12 @@
1
-# [POGZ]
1
+# POGZ
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.40 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
POLRMT.md
... ...
@@ -1,11 +1,12 @@
1
-# [POLRMT]
1
+# POLRMT
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
POR.md
... ...
@@ -1,11 +1,12 @@
1
-# [POR]
1
+# POR
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
POT1.md
... ...
@@ -1,17 +1,18 @@
1
-# [POT1]
1
+# POT1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7 7
|MCL |1 |high-confidence MCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|3.32 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PPP6R2.md
... ...
@@ -1,11 +1,12 @@
1
-# [PPP6R2]
1
+# PPP6R2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PREX1.md
... ...
@@ -1,11 +1,12 @@
1
-# [PREX1]
1
+# PREX1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PRKCB.md
... ...
@@ -1,11 +1,12 @@
1
-# [PRKCB]
1
+# PRKCB
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.60 |
15 16
|DLBCL |Chapuy cohort |3.42 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PRKCD.md
... ...
@@ -1,11 +1,12 @@
1
-# [PRKCD]
1
+# PRKCD
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |1.30 |
14 15
|BL |Panea cohort |5.90 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PRKDC.md
... ...
@@ -1,12 +1,13 @@
1
-# [PRKDC]
1
+# PRKDC
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene |
8 8
|FL |2 |relevance in FL not firmly established|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |6.41 |
17 18
|FL |GAMBL genomes |3.00 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PRPS1.md
... ...
@@ -1,11 +1,12 @@
1
-# [PRPS1]
1
+# PRPS1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.20 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PRSS22.md
... ...
@@ -1,11 +1,12 @@
1
-# [PRSS22]
1
+# PRSS22
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RB1.md
... ...
@@ -1,12 +1,13 @@
1
-# [RB1]
1
+# RB1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|MCL |1 |high-confidence MCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |3.85 |
17 18
|MCL |GAMBL genomes |0.47 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RBM6.md
... ...
@@ -1,17 +1,18 @@
1
-# [RBM6]
1
+# RBM6
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|0.46 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RCC.md
... ...
@@ -1,11 +1,12 @@
1
-# [RCC]
1
+# RCC
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
RET.md
... ...
@@ -1,11 +1,12 @@
1
-# [RET]
1
+# RET
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
REV3L.md
... ...
@@ -1,11 +1,12 @@
1
-# [REV3L]
1
+# REV3L
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RFTN1.md
... ...
@@ -1,11 +1,12 @@
1
-# [RFTN1]
1
+# RFTN1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.40 |
15 16
|DLBCL |Chapuy cohort |4.70 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RFX7.md
... ...
@@ -1,12 +1,13 @@
1
-# [RFX7]
1
+# RFX7
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |3.40 |
19 20
|DLBCL |Chapuy cohort |4.70 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RFXAP.md
... ...
@@ -1,11 +1,12 @@
1
-# [RFXAP]
1
+# RFXAP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.60 |
15 16
|DLBCL |Chapuy cohort | NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RHEX.md
... ...
@@ -1,11 +1,12 @@
1
-# [RHEX]
1
+# RHEX
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
RHOA.md
... ...
@@ -1,12 +1,13 @@
1
-# [RHOA]
1
+# RHOA
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort | 3.30 |
19 20
|DLBCL |Chapuy cohort | 5.13 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RHOH.md
... ...
@@ -1,11 +1,12 @@
1
-# [RHOH]
1
+# RHOH
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.10 |
15 16
|DLBCL |Chapuy cohort | NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ROBO2.md
... ...
@@ -1,17 +1,18 @@
1
-# [ROBO2]
1
+# ROBO2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|1.9 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RRAGC.md
... ...
@@ -1,12 +1,13 @@
1
-# [RRAGC]
1
+# RRAGC
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|FL |1 |high-confidence FL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort | 0.43 |
17 18
|FL |GAMBL genomes |10.85 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SAL3.md
... ...
@@ -1,11 +1,12 @@
1
-# [SAL3]
1
+# SAL3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |NA |
14 15
|BL |Panea cohort |NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|
19 20
SALL3.md
... ...
@@ -1,12 +1,13 @@
1
-# [SALL3]
1
+# SALL3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established |
8 8
|MCL |2 |relevance in MCL not firmly established|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -15,7 +16,7 @@
15 16
|BL |Panea cohort | NA |
16 17
|MCL |GAMBL genomes |0.95 |
17 18
18
-## Mutation pattern
19
+## Mutation pattern and selective pressure estimates
19 20
20 21
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21 22
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SAMD9L.md
... ...
@@ -1,11 +1,12 @@
1
-# [SAMD9L]
1
+# SAMD9L
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.40 |
15 16
|DLBCL |Chapuy cohort |1.71 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SAPS2.md
... ...
@@ -1,11 +1,12 @@
1
-# [SAPS2]
1
+# SAPS2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |NA |
14 15
|BL |Panea cohort |NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|
19 20
SARM1.md
... ...
@@ -1,11 +1,12 @@
1
-# [SARM1]
1
+# SARM1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.70 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SBF1.md
... ...
@@ -1,11 +1,12 @@
1
-# [SBF1]
1
+# SBF1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SEL1L3.md
... ...
@@ -1,11 +1,12 @@
1
-# [SEL1L3]
1
+# SEL1L3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.20 |
15 16
|DLBCL |Chapuy cohort | NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SEPT10.md
... ...
@@ -1,11 +1,12 @@
1
-# [SEPT10]
1
+# SEPT10
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |2.10 |
14 15
|BL |Panea cohort |2.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SEPTIN9.md
... ...
@@ -1,11 +1,12 @@
1
-# [SEPTIN9]
1
+# SEPTIN9
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |NA |
15 16
|DLBCL |Chapuy cohort |NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|
20 21
SERPINA9.md
... ...
@@ -1,11 +1,12 @@
1
-# [SERPINA9]
1
+# SERPINA9
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.90 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SESN1.md
... ...
@@ -1,17 +1,18 @@
1
-# [SESN1]
1
+# SESN1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|0.23 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SETD1B.md
... ...
@@ -1,11 +1,12 @@
1
-# [SETD1B]
1
+# SETD1B
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | 5.81 |
15 16
|DLBCL |Chapuy cohort | NA |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SETD2.md
... ...
@@ -1,11 +1,12 @@
1
-# [SETD2]
1
+# SETD2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.60 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SETD5.md
... ...
@@ -1,11 +1,12 @@
1
-# [SETD5]
1
+# SETD5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |3.20 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SF3B1.md
... ...
@@ -1,12 +1,13 @@
1
-# [SF3B1]
1
+# SF3B1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |2.00 |
19 20
|DLBCL |Chapuy cohort |2.99 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SGK1.md
... ...
@@ -1,13 +1,14 @@
1
-# [SGK1]
1
+# SGK1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 9
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort |12.82 |
21 22
|FL |GAMBL genomes | 6.00 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SHANK1.md
... ...
@@ -1,11 +1,12 @@
1
-# [SHANK1]
1
+# SHANK1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SHROOM3.md
... ...
@@ -1,17 +1,18 @@
1
-# [SHROOM3]
1
+# SHROOM3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.15 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SI.md
... ...
@@ -1,17 +1,18 @@
1
-# [SI]
1
+# SI
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|1.42 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SIAH2.md
... ...
@@ -1,11 +1,12 @@
1
-# [SIAH2]
1
+# SIAH2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SIN3A.md
... ...
@@ -1,12 +1,13 @@
1
-# [SIN3A]
1
+# SIN3A
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort | 3.00 |
19 20
|DLBCL |Chapuy cohort | 3.85 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SLC29A2.md
... ...
@@ -1,11 +1,12 @@
1
-# [SLC29A2]
1
+# SLC29A2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SLC34A2.md
... ...
@@ -1,11 +1,12 @@
1
-# [SLC34A2]
1
+# SLC34A2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.40 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SMARCA4.md
... ...
@@ -1,6 +1,6 @@
1
-# [SMARCA4]
1
+# SMARCA4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
... ...
@@ -8,7 +8,8 @@
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9 9
|FL |1 |high-confidence FL gene |
10 10
|MCL |1 |high-confidence MCL gene |
11
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 13
13 14
|Entity|source |frequency (%)|
14 15
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +23,7 @@
22 23
|FL |GAMBL genomes | 4.16 |
23 24
|MCL |GAMBL genomes | 4.74 |
24 25
25
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
26 27
27 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SMARCB1.md
... ...
@@ -1,17 +1,18 @@
1
-# [SMARCB1]
1
+# SMARCB1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|1.9 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SMC1A.md
... ...
@@ -1,17 +1,18 @@
1
-# [SMC1A]
1
+# SMC1A
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|0 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SMEK1.md
... ...
@@ -1,11 +1,12 @@
1
-# [SMEK1]
1
+# SMEK1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.90 |
15 16
|DLBCL |Chapuy cohort |2.99 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SPEN.md
... ...
@@ -1,11 +1,12 @@
1
-# [SPEN]
1
+# SPEN
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | 7.41 |
15 16
|DLBCL |Chapuy cohort | 9.83 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
STAT6.md
... ...
@@ -1,15 +1,16 @@
1 1
# STAT6
2
-
2
+## Overview
3 3
The STAT6 gene, which encodes a transcription factor involved in the JAK-STAT signaling pathway, plays a significant role in the pathogenesis of various lymphomas, including diffuse large B-cell lymphoma (DLBCL). Below is a summary of the common mutations in the STAT6 gene identified in DLBCL. Mutations in the DNA binding domain of STAT6 are common in PMBCL and more rare in DLBCL.
4 4
5
-## Mutation tier
5
+## Relevance tier by entity
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9 9
|BL |2 |relevance in BL not firmly established|
10 10
|DLBCL |1 |high-confidence DLBCL gene |
11 11
|FL |1 |high-confidence FL gene |
12
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 14
14 15
|Entity|source |frequency (%)|
15 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +23,7 @@ The STAT6 gene, which encodes a transcription factor involved in the JAK-STAT si
22 23
|DLBCL |Chapuy cohort | 4.70 |
23 24
|FL |GAMBL genomes |15.94 |
24 25
25
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
26 27
27 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
... ...
@@ -62,4 +63,4 @@ View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/
62 63
63 64
## References
64 65
65
-1. *Morin RD, Assouline S, Alcaide M, Mohajeri A, Johnston RL, Chong L, Grewal J, Yu S, Fornika D, Bushell K, Nielsen TH, Petrogiannis-Haliotis T, Crump M, Tosikyan A, Grande BM, MacDonald D, Rousseau C, Bayat M, Sesques P, Froment R, Albuquerque M, Monczak Y, Oros KK, Greenwood C, Riazalhosseini Y, Arseneault M, Camlioglu E, Constantin A, Pan-Hammarstrom Q, Peng R, Mann KK, Johnson NA. Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas. Clin Cancer Res. 2016 May 1;22(9):2290-300. doi: 10.1158/1078-0432.CCR-15-2123. Epub 2015 Dec 8. PMID: 26647218.*
... ...
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0
+1. *Morin RD, Assouline S, Alcaide M, Mohajeri A, Johnston RL, Chong L, Grewal J, Yu S, Fornika D, Bushell K, Nielsen TH, Petrogiannis-Haliotis T, Crump M, Tosikyan A, Grande BM, MacDonald D, Rousseau C, Bayat M, Sesques P, Froment R, Albuquerque M, Monczak Y, Oros KK, Greenwood C, Riazalhosseini Y, Arseneault M, Camlioglu E, Constantin A, Pan-Hammarstrom Q, Peng R, Mann KK, Johnson NA. Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas. Clin Cancer Res. 2016 May 1;22(9):2290-300. doi: 10.1158/1078-0432.CCR-15-2123. Epub 2015 Dec 8. PMID: 26647218.*
SYK.md
... ...
@@ -1,11 +1,12 @@
1
-# [SYK]
1
+# SYK
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.80 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SYNCRIP.md
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@@ -1,11 +1,12 @@
1
-# [SYNCRIP]
1
+# SYNCRIP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |2.5 |
14 15
|BL |Panea cohort |5.0 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SYNE1.md
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@@ -1,17 +1,18 @@
1
-# [SYNE1]
1
+# SYNE1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7 7
|MCL |1 |high-confidence MCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|4.74 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SYNGAP1.md
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@@ -1,11 +1,12 @@
1
-# [SYNGAP1]
1
+# SYNGAP1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SYPL1.md
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@@ -1,11 +1,12 @@
1
-# [SYPL1]
1
+# SYPL1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.40 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TAF1.md
... ...
@@ -1,11 +1,12 @@
1
-# [TAF1]
1
+# TAF1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.00 |
15 16
|DLBCL |Chapuy cohort |3.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TAP1.md
... ...
@@ -1,11 +1,12 @@
1
-# [TAP1]
1
+# TAP1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort | NA |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TBC1D4.md
... ...
@@ -1,11 +1,12 @@
1
-# [TBC1D4]
1
+# TBC1D4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.70 |
15 16
|DLBCL |Chapuy cohort |5.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TBL1XR1.md
... ...
@@ -1,13 +1,14 @@
1
-# [TBL1XR1]
1
+# TBL1XR1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|FL |1 |high-confidence FL gene |
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort | 8.12 |
21 22
|FL |GAMBL genomes | 3.93 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|