CD22.md
... ...
@@ -1,11 +1,12 @@
1
-# [CD22]
1
+# CD22
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.80 |
15 16
|DLBCL |Chapuy cohort |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD274.md
... ...
@@ -1,11 +1,12 @@
1
-# [CD274]
1
+# CD274
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |2.56 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD36.md
... ...
@@ -1,11 +1,12 @@
1
-# [CD36]
1
+# CD36
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 |2.80 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD44.md
... ...
@@ -1,11 +1,12 @@
1
-# [CD44]
1
+# CD44
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD58.md
... ...
@@ -1,12 +1,13 @@
1
-# [CD58]
1
+# CD58
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort | 2.80 |
19 20
|DLBCL |Chapuy cohort | 6.84 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD70.md
... ...
@@ -1,13 +1,14 @@
1
-# [CD70]
1
+# CD70
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 |7.69 |
21 22
|FL |GAMBL genomes |1.15 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD74.md
... ...
@@ -1,11 +1,12 @@
1
-# [CD74]
1
+# CD74
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.60 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD79A.md
... ...
@@ -1,11 +1,12 @@
1
-# [CD79A]
1
+# CD79A
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD79B.md
... ...
@@ -1,13 +1,14 @@
1
-# [CD79B]
1
+# CD79B
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 |15.38 |
21 22
|FL |GAMBL genomes | 2.77 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CD83.md
... ...
@@ -1,15 +1,17 @@
1 1
# CD83
2
+## Overview
2 3
3 4
CD83 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.
4 5
5
-## Mutation tier
6
+## Relevance tier by entity
6 7
7 8
|Entity|Tier|Description |
8 9
|:------:|:----:|--------------------------------------|
9 10
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10 11
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11 12
|FL |1-a | aSHM target and high-confidence FL gene |
12
-## Mutation incidence
13
+
14
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 15
14 16
|Entity|source |frequency (%)|
15 17
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +24,7 @@ CD83 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
22 24
|DLBCL |Chapuy cohort |7.26 |
23 25
|FL |GAMBL genomes |1.85 |
24 26
25
-## Mutation pattern
27
+## Mutation pattern and selective pressure estimates
26 28
27 29
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 30
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CDC73.md
... ...
@@ -1,12 +1,13 @@
1
-# [CDC73]
1
+# CDC73
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 |0.70 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CDH17.md
... ...
@@ -1,11 +1,12 @@
1
-# [CDH17]
1
+# CDH17
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CDH8.md
... ...
@@ -1,17 +1,18 @@
1
-# [CDH8]
1
+# CDH8
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CDH9.md
... ...
@@ -1,11 +1,12 @@
1
-# [CDH9]
1
+# CDH9
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 |2.56 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CDKN2A.md
... ...
@@ -1,12 +1,13 @@
1
-# [CDKN2A]
1
+# CDKN2A
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 |1.00 |
19 20
|DLBCL |Chapuy cohort |1.71 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|Isoform |aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:---------------:|:----:|:---------------------:|:----------------:|:----------------:|
CDKN2C.md
... ...
@@ -1,11 +1,12 @@
1
-# [CDKN2C]
1
+# CDKN2C
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 |3.40 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CHD1.md
... ...
@@ -1,11 +1,12 @@
1
-# [CHD1]
1
+# CHD1
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CHD4.md
... ...
@@ -1,11 +1,12 @@
1
-# [CHD4]
1
+# CHD4
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CHD8.md
... ...
@@ -1,12 +1,13 @@
1
-# [CHD8]
1
+# CHD8
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 | 2.90 |
19 20
|DLBCL |Chapuy cohort | 2.99 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CHST2.md
... ...
@@ -1,11 +1,12 @@
1
-# [CHST2]
1
+# CHST2
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CIITA.md
... ...
@@ -1,13 +1,14 @@
1 1
# CIITA
2
-
2
+## Overview
3 3
CIITA 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.
4 4
5
-## Mutation tier
5
+## Relevance tier by entity
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
10
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@ CIITA is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 17
|DLBCL |Reddy cohort |4.30 |
17 18
|DLBCL |Chapuy cohort |4.27 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CILP.md
... ...
@@ -1,17 +1,18 @@
1
-# [CILP]
1
+# CILP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|0.46 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CNOT2.md
... ...
@@ -1,11 +1,12 @@
1
-# [CNOT2]
1
+# CNOT2
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CNTNAP5.md
... ...
@@ -1,11 +1,12 @@
1
-# [CNTNAP5]
1
+# CNTNAP5
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 |4.00 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
COL11A1.md
... ...
@@ -1,17 +1,18 @@
1
-# [COL11A1]
1
+# COL11A1
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
COL16A1.md
... ...
@@ -1,17 +1,18 @@
1
-# [COL16A1]
1
+# COL16A1
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|0.95 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
COL4A2.md
... ...
@@ -1,11 +1,12 @@
1
-# [COL4A2]
1
+# COL4A2
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
COQ7.md
... ...
@@ -1,11 +1,12 @@
1
-# [COQ7]
1
+# COQ7
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CPNE8.md
... ...
@@ -1,17 +1,18 @@
1
-# [CPNE8]
1
+# CPNE8
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CPXM2.md
... ...
@@ -1,11 +1,12 @@
1
-# [CPXM2]
1
+# CPXM2
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CREBBP.md
... ...
@@ -1,13 +1,14 @@
1 1
# CREBBP
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 |16.67 |
21 22
|FL |GAMBL genomes |65.13 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CRIP1.md
... ...
@@ -1,11 +1,12 @@
1
-# [CRIP1]
1
+# CRIP1
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 |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CTCF.md
... ...
@@ -1,11 +1,12 @@
1
-# [CTCF]
1
+# CTCF
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 |1.7 |
14 15
|BL |Panea cohort |6.9 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CTNNA2.md
... ...
@@ -1,17 +1,18 @@
1
-# [CTNNA2]
1
+# CTNNA2
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CTSS.md
... ...
@@ -1,17 +1,18 @@
1
-# [CTSS]
1
+# CTSS
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|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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CXCR4.md
... ...
@@ -1,14 +1,17 @@
1 1
# CXCR4
2
+## Overview
3
+
2 4
CXCR4 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.
3 5
4
-## Mutation tier
6
+## Relevance tier by entity
5 7
6 8
|Entity|Tier|Description |
7 9
|:------:|:----:|--------------------------------------|
8 10
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9 11
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 12
|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
11
-## Mutation incidence
13
+
14
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 15
13 16
|Entity|source |frequency (%)|
14 17
|:------:|:---------------------:|:-------------:|
... ...
@@ -21,7 +24,7 @@ CXCR4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
21 24
|DLBCL |Chapuy cohort |2.56 |
22 25
|FL |GAMBL genomes |3.46 |
23 26
24
-## Mutation pattern
27
+## Mutation pattern and selective pressure estimates
25 28
26 29
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27 30
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CXCR5.md
... ...
@@ -1,12 +1,14 @@
1 1
# CXCR5
2
+## Overview
2 3
CXCR5 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.
3 4
4
-## Mutation tier
5
+## Relevance tier by entity
5 6
6 7
|Entity|Tier|Description |
7 8
|:------:|:----:|--------------------------|
8 9
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
11 13
|Entity|source |frequency (%)|
12 14
|:------:|:--------------:|:-------------:|
... ...
@@ -15,7 +17,7 @@ CXCR5 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 17
|DLBCL |Reddy cohort |2.10 |
16 18
|DLBCL |Chapuy cohort |1.71 |
17 19
18
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
19 21
20 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
21 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CYB5D1.md
... ...
@@ -1,11 +1,12 @@
1
-# [CYB5D1]
1
+# CYB5D1
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CYP2A6.md
... ...
@@ -1,17 +1,18 @@
1
-# [CYP2A6]
1
+# CYP2A6
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|0.23 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CYP4F22.md
... ...
@@ -1,11 +1,12 @@
1
-# [CYP4F22]
1
+# CYP4F22
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
DAZAP1.md
... ...
@@ -1,12 +1,13 @@
1 1
# DAZAP1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|MCL |1 |high-confidence MCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |0.43 |
17 18
|MCL |GAMBL genomes |4.27 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
DCAF6.md
... ...
@@ -1,11 +1,12 @@
1
-# [DCAF6]
1
+# DCAF6
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.30 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
DDX10.md
... ...
@@ -1,11 +1,12 @@
1
-# [DDX10]
1
+# DDX10
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.80 |
15 16
|DLBCL |Chapuy cohort |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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
DDX3X.md
... ...
@@ -1,13 +1,14 @@
1
-# [DDX3X]
1
+# DDX3X
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
|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
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 | 2.54 |
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
DHDH.md
... ...
@@ -1,17 +1,18 @@
1
-# [DHDH]
1
+# DHDH
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
|:------:|:----:|:---------------------:|:----------------:|:----------------:|