PCBP1.md
... ...
@@ -1,12 +1,13 @@
1
-# [PCBP1]
1
+# PCBP1
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 | 2.40 |
19 20
|DLBCL |Chapuy cohort | 1.71 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PCDHA11.md
... ...
@@ -1,11 +1,12 @@
1
-# [PCDHA11]
1
+# PCDHA11
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PCDHB11.md
... ...
@@ -1,11 +1,12 @@
1
-# [PCDHB11]
1
+# PCDHB11
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PCDHB2.md
... ...
@@ -1,17 +1,18 @@
1
-# [PCDHB2]
1
+# PCDHB2
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|0.47 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PCLO.md
... ...
@@ -1,12 +1,13 @@
1
-# [PCLO]
1
+# PCLO
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 |23.08 |
17 18
|FL |GAMBL genomes | 9.24 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PDCD11.md
... ...
@@ -1,11 +1,12 @@
1
-# [PDCD11]
1
+# PDCD11
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PDS5B.md
... ...
@@ -1,12 +1,13 @@
1
-# [PDS5B]
1
+# PDS5B
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 |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 |2.14 |
17 18
|FL |GAMBL genomes |1.62 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PDZRN3.md
... ...
@@ -1,11 +1,12 @@
1
-# [PDZRN3]
1
+# PDZRN3
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 |9.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PHF6.md
... ...
@@ -1,12 +1,13 @@
1
-# [PHF6]
1
+# PHF6
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 |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 |1.40 |
19 20
|DLBCL |Chapuy cohort |0.85 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PIK3CD.md
... ...
@@ -1,11 +1,12 @@
1
-# [PIK3CD]
1
+# PIK3CD
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PIK3R1.md
... ...
@@ -1,12 +1,13 @@
1
-# [PIK3R1]
1
+# PIK3R1
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 |2.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PIM1.md
... ...
@@ -1,13 +1,16 @@
1
+# PIM1
2
+## Overview
1 3
PIM1 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 @@ PIM1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
20 23
|DLBCL |Chapuy cohort |23.93 |
21 24
|FL |GAMBL genomes | 9.24 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PIM2.md
... ...
@@ -1,11 +1,14 @@
1
+# PIM2
2
+## Overview
1 3
PIM2 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 @@ PIM2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
14 17
|DLBCL |Reddy cohort |4.00 |
15 18
|DLBCL |Chapuy cohort |3.85 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
POU2AF1.md
... ...
@@ -1,13 +1,16 @@
1
+# POU2AF1
2
+## Overview
1 3
POU2AF1 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 |high-confidence DLBCL gene, hypermutated|
8 10
|FL |1-a |high-confidence FL gene, hypermutated |
9 11
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:--------------:|:-------------:|
... ...
@@ -17,7 +20,7 @@ POU2AF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
17 20
|DLBCL |Chapuy cohort | 5.56 |
18 21
|FL |GAMBL genomes |12.24 |
19 22
20
-## Mutation pattern
23
+## Mutation pattern and selective pressure estimates
21 24
22 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23 26
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
POU2F2.md
... ...
@@ -1,12 +1,13 @@
1
-# [POU2F2]
1
+# POU2F2
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 |6.41 |
17 18
|FL |GAMBL genomes |6.24 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PPP1R9B.md
... ...
@@ -1,11 +1,12 @@
1
-# [PPP1R9B]
1
+# PPP1R9B
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 |0.70 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PPP4C.md
... ...
@@ -1,17 +1,18 @@
1
-# [PPP4C]
1
+# PPP4C
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|2.08 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PRDM1.md
... ...
@@ -1,12 +1,13 @@
1
-# [PRDM1]
1
+# PRDM1
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 | 5.41 |
19 20
|DLBCL |Chapuy cohort | 8.55 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTEN.md
... ...
@@ -1,12 +1,13 @@
1
-# [PTEN]
1
+# PTEN
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 |3.10 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTMA.md
... ...
@@ -1,11 +1,12 @@
1
-# [PTMA]
1
+# PTMA
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 |0.20 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTPN1.md
... ...
@@ -1,11 +1,12 @@
1
-# [PTPN1]
1
+# PTPN1
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 |1.40 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTPN23.md
... ...
@@ -1,11 +1,12 @@
1
-# [PTPN23]
1
+# PTPN23
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTPN6.md
... ...
@@ -1,11 +1,12 @@
1
-# [PTPN6]
1
+# PTPN6
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 |2.90 |
15 16
|DLBCL |Chapuy cohort |5.13 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTPRD.md
... ...
@@ -1,12 +1,13 @@
1
-# [PTPRD]
1
+# PTPRD
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 |5.56 |
17 18
|FL |GAMBL genomes |3.70 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTPRK.md
... ...
@@ -1,11 +1,12 @@
1
-# [PTPRK]
1
+# PTPRK
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 |3.30 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PTPRN.md
... ...
@@ -1,11 +1,12 @@
1
-# [PTPRN]
1
+# PTPRN
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PXDNL.md
... ...
@@ -1,11 +1,12 @@
1
-# [PXDNL]
1
+# PXDNL
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 |9.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
PZP.md
... ...
@@ -1,17 +1,18 @@
1
-# [PZP]
1
+# PZP
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|0.92 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RAC2.md
... ...
@@ -1,12 +1,13 @@
1
-# [RAC2]
1
+# RAC2
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 |1.20 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RAD9A.md
... ...
@@ -1,11 +1,12 @@
1
-# [RAD9A]
1
+# RAD9A
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 |0.50 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RANBP6.md
... ...
@@ -1,11 +1,12 @@
1
-# [RANBP6]
1
+# RANBP6
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RARA.md
... ...
@@ -1,11 +1,12 @@
1
-# [RARA]
1
+# RARA
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RBP3.md
... ...
@@ -1,11 +1,12 @@
1
-# [RBP3]
1
+# RBP3
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RNF144B.md
... ...
@@ -1,11 +1,12 @@
1
-# [RNF144B]
1
+# RNF144B
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
-## 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 |0.40 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RPL10.md
... ...
@@ -1,11 +1,12 @@
1
-# [RPL10]
1
+# RPL10
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RPL22.md
... ...
@@ -1,11 +1,12 @@
1
-# [RPL22]
1
+# RPL22
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
RUBCNL.md
... ...
@@ -1,11 +1,12 @@
1
-# [RUBCNL]
1
+# RUBCNL
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
RUNX1.md
... ...
@@ -1,11 +1,12 @@
1
-# [RUNX1]
1
+# RUNX1
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 |0.50 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
S1PR1.md
... ...
@@ -1,17 +1,18 @@
1
-# [S1PR1]
1
+# S1PR1
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|5.69 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
S1PR2.md
... ...
@@ -1,13 +1,16 @@
1
+# S1PR2
2
+## Overview
1 3
S1PR2 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 @@ S1PR2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
20 23
|DLBCL |Chapuy cohort |2.56 |
21 24
|FL |GAMBL genomes |6.24 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SNTB2.md
... ...
@@ -1,11 +1,12 @@
1
-# [SNTB2]
1
+# SNTB2
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 |0.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SOCS1.md
... ...
@@ -1,13 +1,14 @@
1
-# [SOCS1]
1
+# SOCS1
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 | 4.70 |
21 22
|FL |GAMBL genomes | 9.70 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SP140.md
... ...
@@ -1,17 +1,18 @@
1
-# [SP140]
1
+# SP140
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|5.21 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SP3.md
... ...
@@ -1,11 +1,12 @@
1
-# [SP3]
1
+# SP3
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SRRM2.md
... ...
@@ -1,12 +1,13 @@
1
-# [SRRM2]
1
+# SRRM2
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 |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 |6.84 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ST6GAL1.md
... ...
@@ -1,11 +1,12 @@
1
-# [ST6GAL1]
1
+# ST6GAL1
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
STAB2.md
... ...
@@ -1,17 +1,18 @@
1
-# [STAB2]
1
+# STAB2
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|2.54 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
STAT3.md
... ...
@@ -1,12 +1,13 @@
1
-# [STAT3]
1
+# STAT3
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 |7.26 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
STAT5B.md
... ...
@@ -1,11 +1,12 @@
1
-# [STAT5B]
1
+# STAT5B
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TBC1D26.md
... ...
@@ -1,17 +1,18 @@
1
-# [TBC1D26]
1
+# TBC1D26
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TBC1D9B.md
... ...
@@ -1,11 +1,12 @@
1
-# [TBC1D9B]
1
+# TBC1D9B
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TCF3.md
... ...
@@ -1,11 +1,12 @@
1
-# [TCF3]
1
+# TCF3
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
-## 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 |11.00 |
14 15
|BL |Panea cohort | 9.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TCL1A.md
... ...
@@ -1,13 +1,14 @@
1
-# [TCL1A]
1
+# TCL1A
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|BL |1-a | aSHM target and high-confidence BL gene |
8 8
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 9
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -19,7 +20,7 @@
19 20
|DLBCL |Reddy cohort |2.80 |
20 21
|DLBCL |Chapuy cohort |2.99 |
21 22
22
-## Mutation pattern
23
+## Mutation pattern and selective pressure estimates
23 24
24 25
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
25 26
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TERT.md
... ...
@@ -1,17 +1,18 @@
1
-# [TERT]
1
+# TERT
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|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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TET2.md
... ...
@@ -1,12 +1,13 @@
1
-# [TET2]
1
+# TET2
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 | 7.41 |
19 20
|DLBCL |Chapuy cohort | 5.98 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TFAP4.md
... ...
@@ -1,11 +1,12 @@
1
-# [TFAP4]
1
+# TFAP4
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
-## 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 |10.60 |
14 15
|BL |Panea cohort | 9.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TGFBR2.md
... ...
@@ -1,11 +1,12 @@
1
-# [TGFBR2]
1
+# TGFBR2
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 |1.28 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TIGD6.md
... ...
@@ -1,11 +1,12 @@
1
-# [TIGD6]
1
+# TIGD6
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TIPARP.md
... ...
@@ -1,11 +1,12 @@
1
-# [TIPARP]
1
+# TIPARP
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 | 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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TLR2.md
... ...
@@ -1,12 +1,13 @@
1
-# [TLR2]
1
+# TLR2
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
|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 |2.99 |
17 18
|MCL |GAMBL genomes |0.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TMEM30A.md
... ...
@@ -1,13 +1,14 @@
1
-# [TMEM30A]
1
+# TMEM30A
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 |5.56 |
21 22
|FL |GAMBL genomes |0.92 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TMSB4X.md
... ...
@@ -1,13 +1,16 @@
1
+# TMSB4X
2
+## Overview
1 3
TMSB4X 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 @@ TMSB4X is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
20 23
|DLBCL |Chapuy cohort |18.38 |
21 24
|FL |GAMBL genomes | 4.39 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TNFAIP3.md
... ...
@@ -1,13 +1,14 @@
1
-# [TNFAIP3]
1
+# TNFAIP3
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 |12.39 |
21 22
|FL |GAMBL genomes | 4.85 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TNFRSF14.md
... ...
@@ -1,13 +1,14 @@
1
-# [TNFRSF14]
1
+# TNFRSF14
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 |12.82 |
21 22
|FL |GAMBL genomes |40.42 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TOP2A.md
... ...
@@ -1,11 +1,12 @@
1
-# [TOP2A]
1
+# TOP2A
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TOX.md
... ...
@@ -1,12 +1,13 @@
1
-# [TOX]
1
+# TOX
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 |4.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TP53.md
... ...
@@ -1,6 +1,6 @@
1
-# [TP53]
1
+# TP53
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 | 6.93 |
23 24
|MCL |GAMBL genomes | 9.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TPP1.md
... ...
@@ -1,17 +1,18 @@
1
-# [TPP1]
1
+# TPP1
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|0.92 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TPST2.md
... ...
@@ -1,11 +1,12 @@
1
-# [TPST2]
1
+# TPST2
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TRAF3.md
... ...
@@ -1,11 +1,12 @@
1
-# [TRAF3]
1
+# TRAF3
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 |0.43 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TRAF6.md
... ...
@@ -1,11 +1,12 @@
1
-# [TRAF6]
1
+# TRAF6
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TRIP12.md
... ...
@@ -1,11 +1,12 @@
1
-# [TRIP12]
1
+# TRIP12
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TRRAP.md
... ...
@@ -1,11 +1,12 @@
1
-# [TRRAP]
1
+# TRRAP
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 |5.98 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
TTN.md
... ...
@@ -1,11 +1,12 @@
1
-# [TTN]
1
+# TTN
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
UBE2A.md
... ...
@@ -1,12 +1,13 @@
1
-# [UBE2A]
1
+# UBE2A
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 |3.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
UBE2J1.md
... ...
@@ -1,11 +1,12 @@
1
-# [UBE2J1]
1
+# UBE2J1
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 |0.80 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
UBR5.md
... ...
@@ -1,12 +1,13 @@
1
-# [UBR5]
1
+# UBR5
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
|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 |5.13 |
17 18
|MCL |GAMBL genomes |9.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
UNC5B.md
... ...
@@ -1,11 +1,12 @@
1
-# [UNC5B]
1
+# UNC5B
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 |1.80 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
UNC5C.md
... ...
@@ -1,11 +1,12 @@
1
-# [UNC5C]
1
+# UNC5C
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
UNC5D.md
... ...
@@ -1,11 +1,12 @@
1
-# [UNC5D]
1
+# UNC5D
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 |1.80 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
USP7.md
... ...
@@ -1,12 +1,13 @@
1
-# [USP7]
1
+# USP7
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 |1.10 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
VMA21.md
... ...
@@ -1,17 +1,18 @@
1
-# [VMA21]
1
+# VMA21
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7 7
|FL |1 |high-confidence FL 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
|FL |GAMBL genomes|5.08 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
VPS13B.md
... ...
@@ -1,11 +1,12 @@
1
-# [VPS13B]
1
+# VPS13B
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 |5.71 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
VWA7.md
... ...
@@ -1,11 +1,12 @@
1
-# [VWA7]
1
+# VWA7
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WAC.md
... ...
@@ -1,11 +1,12 @@
1
-# [WAC]
1
+# WAC
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WDFY3.md
... ...
@@ -1,11 +1,12 @@
1
-# [WDFY3]
1
+# WDFY3
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WDR7.md
... ...
@@ -1,11 +1,12 @@
1
-# [WDR7]
1
+# WDR7
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 |0.40 |
14 15
|BL |Panea cohort |6.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WDR90.md
... ...
@@ -1,11 +1,12 @@
1
-# [WDR90]
1
+# WDR90
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WEE1.md
... ...
@@ -1,11 +1,14 @@
1
+# WEE1
2
+## Overview
1 3
WEE1 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 @@ WEE1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
14 17
|DLBCL |Reddy cohort |1.60 |
15 18
|DLBCL |Chapuy cohort |1.71 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WHAMM.md
... ...
@@ -1,11 +1,12 @@
1
-# [WHAMM]
1
+# WHAMM
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WNK1.md
... ...
@@ -1,12 +1,13 @@
1
-# [WNK1]
1
+# WNK1
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 |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 | 3.70 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
WNK2.md
... ...
@@ -1,11 +1,12 @@
1
-# [WNK2]
1
+# WNK2
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 |10.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
XBP1.md
... ...
@@ -1,11 +1,12 @@
1
-# [XBP1]
1
+# XBP1
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 | 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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
XIRP2.md
... ...
@@ -1,17 +1,18 @@
1
-# [XIRP2]
1
+# XIRP2
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|3.93 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
XPO1.md
... ...
@@ -1,11 +1,12 @@
1
-# [XPO1]
1
+# XPO1
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 |1.40 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
YY1.md
... ...
@@ -1,11 +1,12 @@
1
-# [YY1]
1
+# YY1
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
YY1AP1.md
... ...
@@ -1,11 +1,12 @@
1
-# [YY1AP1]
1
+# YY1AP1
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZAN.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZAN]
1
+# ZAN
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
ZBTB7A.md
... ...
@@ -1,12 +1,13 @@
1
-# [ZBTB7A]
1
+# ZBTB7A
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 |1.30 |
19 20
|DLBCL |Chapuy cohort |1.71 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZC3H12A.md
... ...
@@ -1,12 +1,13 @@
1
-# [ZC3H12A]
1
+# ZC3H12A
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 |4.70 |
17 18
|FL |GAMBL genomes |0.46 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZCCHC7.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZCCHC7]
1
+# ZCCHC7
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 |0.40 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZEB2.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZEB2]
1
+# ZEB2
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 |3.70 |
15 16
|DLBCL |Chapuy cohort |5.98 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZFAT.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZFAT]
1
+# ZFAT
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 |2.56 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZFP36L1.md
... ...
@@ -1,12 +1,15 @@
1
+# ZFP36L1
2
+## Overview
1 3
ZFP36L1 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 @@ ZFP36L1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
18 21
|DLBCL |Reddy cohort |5.61 |
19 22
|DLBCL |Chapuy cohort |8.12 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZFX.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZFX]
1
+# ZFX
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 |0.43 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF117.md
... ...
@@ -1,17 +1,18 @@
1
-# [ZNF117]
1
+# ZNF117
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF217.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZNF217]
1
+# ZNF217
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 |2.90 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF229.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZNF229]
1
+# ZNF229
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF292.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZNF292]
1
+# ZNF292
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 |4.30 |
15 16
|DLBCL |Chapuy cohort |5.98 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF296.md
... ...
@@ -1,17 +1,18 @@
1
-# [ZNF296]
1
+# ZNF296
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF423.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZNF423]
1
+# ZNF423
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF608.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZNF608]
1
+# ZNF608
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 |8.11 |
15 16
|DLBCL |Chapuy cohort |7.69 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ZNF85.md
... ...
@@ -1,11 +1,12 @@
1
-# [ZNF85]
1
+# ZNF85
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|