9adef57f980933dc2ba34cfc0dd4cd6f5a39e4e9
DHX15.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [DHX15] |
|
| 1 | +# DHX15 |
|
| 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|0.69 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DHX16.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DHX16] |
|
| 1 | +# DHX16 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DICER1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DICER1] |
|
| 1 | +# DICER1 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DLC1.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [DLC1] |
|
| 1 | +# DLC1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|---------------------------------------| |
| 7 | 7 | |MCL |2 |relevance in MCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:-------------:|:-------------:| |
| 12 | 13 | |MCL |GAMBL genomes|1.42 | |
| 13 | 14 | |
| 14 | -## Mutation pattern |
|
| 15 | +## Mutation pattern and selective pressure estimates |
|
| 15 | 16 | |
| 16 | 17 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 17 | 18 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DLGAP1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DLGAP1] |
|
| 1 | +# DLGAP1 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DNAH5.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DNAH5] |
|
| 1 | +# DNAH5 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort | 6.91 | |
| 15 | 16 | |DLBCL |Chapuy cohort |11.54 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DNM2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DNM2] |
|
| 1 | +# DNM2 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DNMT1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DNMT1] |
|
| 1 | +# DNMT1 |
|
| 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 |1.70 | |
| 14 | 15 | |BL |Panea cohort |5.00 | |
| 15 | 16 | |
| 16 | -## Mutation pattern |
|
| 17 | +## Mutation pattern and selective pressure estimates |
|
| 17 | 18 | |
| 18 | 19 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 19 | 20 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DNMT3A.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DNMT3A] |
|
| 1 | +# DNMT3A |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DOCK1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DOCK1] |
|
| 1 | +# DOCK1 |
|
| 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 | 4.90 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DSG4.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [DSG4] |
|
| 1 | +# DSG4 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |2.40 | |
| 15 | 16 | |DLBCL |Chapuy cohort |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DTX1.md
| ... | ... | @@ -1,14 +1,16 @@ |
| 1 | 1 | # DTX1 |
| 2 | +## Overview |
|
| 2 | 3 | DTX1 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 | |BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous | |
| 9 | 10 | |DLBCL |1-a | aSHM target and high-confidence DLBCL gene | |
| 10 | 11 | |FL |1-a | aSHM target and high-confidence FL gene | |
| 11 | -## Mutation incidence |
|
| 12 | + |
|
| 13 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 12 | 14 | |
| 13 | 15 | |Entity|source |frequency (%)| |
| 14 | 16 | |:------:|:---------------------:|:-------------:| |
| ... | ... | @@ -21,7 +23,7 @@ DTX1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 21 | 23 | |DLBCL |Chapuy cohort |11.54 | |
| 22 | 24 | |FL |GAMBL genomes | 5.54 | |
| 23 | 25 | |
| 24 | -## Mutation pattern |
|
| 26 | +## Mutation pattern and selective pressure estimates |
|
| 25 | 27 | |
| 26 | 28 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 27 | 29 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
DUSP2.md
| ... | ... | @@ -1,13 +1,16 @@ |
| 1 | 1 | # DUSP2 |
| 2 | +## Overview |
|
| 3 | + |
|
| 2 | 4 | DUSP2 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 | |DLBCL |1-a | aSHM target and high-confidence DLBCL gene | |
| 9 | 11 | |FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous | |
| 10 | -## Mutation incidence |
|
| 12 | + |
|
| 13 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 11 | 14 | |
| 12 | 15 | |Entity|source |frequency (%)| |
| 13 | 16 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -17,7 +20,7 @@ DUSP2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 17 | 20 | |DLBCL |Chapuy cohort | 4.27 | |
| 18 | 21 | |FL |GAMBL genomes | 2.31 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
E2F2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [E2F2] |
|
| 1 | +# E2F2 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EBF1.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -EBF1 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. |
|
| 1 | +EBF1 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 | 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 @@ EBF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 20 | 21 | |DLBCL |Chapuy cohort |12.82 | |
| 21 | 22 | |FL |GAMBL genomes | 8.55 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EDNRB.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EDNRB] |
|
| 1 | +# EDNRB |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EEF1A1.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [EEF1A1] |
|
| 1 | +# EEF1A1 |
|
| 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 |11.32 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EHD1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EHD1] |
|
| 1 | +# EHD1 |
|
| 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 |5.90 | |
| 15 | 16 | |
| 16 | -## Mutation pattern |
|
| 17 | +## Mutation pattern and selective pressure estimates |
|
| 17 | 18 | |
| 18 | 19 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 19 | 20 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EIF2AK3.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EIF2AK3] |
|
| 1 | +# EIF2AK3 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |1.50 | |
| 15 | 16 | |DLBCL |Chapuy cohort |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EIF2AK4.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [EIF2AK4] |
|
| 1 | +# EIF2AK4 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EIF2C4.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EIF2C4] |
|
| 1 | +# EIF2C4 |
|
| 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 |
EIF4A1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EIF4A1] |
|
| 1 | +# EIF4A1 |
|
| 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 |5.10 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EML2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EML2] |
|
| 1 | +# EML2 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ENTPD3.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [ENTPD3] |
|
| 1 | +# ENTPD3 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EP300.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [EP300] |
|
| 1 | +# EP300 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------------------| |
| 7 | 7 | |BL |2 |relevance in BL not firmly established| |
| 8 | 8 | |DLBCL |1 |high-confidence DLBCL gene | |
| 9 | 9 | |FL |1 |high-confidence FL gene | |
| 10 | -## Mutation incidence |
|
| 10 | + |
|
| 11 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 11 | 12 | |
| 12 | 13 | |Entity|source |frequency (%)| |
| 13 | 14 | |:------:|:---------------------:|:-------------:| |
| ... | ... | @@ -20,7 +21,7 @@ |
| 20 | 21 | |DLBCL |Chapuy cohort | 8.12 | |
| 21 | 22 | |FL |GAMBL genomes |12.47 | |
| 22 | 23 | |
| 23 | -## Mutation pattern |
|
| 24 | +## Mutation pattern and selective pressure estimates |
|
| 24 | 25 | |
| 25 | 26 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 26 | 27 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EPHB2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EPHB2] |
|
| 1 | +# EPHB2 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EPPK1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EPPK1] |
|
| 1 | +# EPPK1 |
|
| 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 | 7.60 | |
| 14 | 15 | |BL |Panea cohort |15.80 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ERAP1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [ERAP1] |
|
| 1 | +# ERAP1 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ESX1.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [ESX1] |
|
| 1 | +# ESX1 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ETS1.md
| ... | ... | @@ -1,12 +1,15 @@ |
| 1 | +# ETS1 |
|
| 2 | +## Overview |
|
| 1 | 3 | ETS1 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 @@ ETS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 18 | 21 | |DLBCL |Reddy cohort | 4.40 | |
| 19 | 22 | |DLBCL |Chapuy cohort | 5.56 | |
| 20 | 23 | |
| 21 | -## Mutation pattern |
|
| 24 | +## Mutation pattern and selective pressure estimates |
|
| 22 | 25 | |
| 23 | 26 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 24 | 27 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ETV6.md
| ... | ... | @@ -1,11 +1,14 @@ |
| 1 | +# ETV6 |
|
| 2 | +## Overview |
|
| 1 | 3 | ETV6 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 @@ ETV6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 14 | 17 | |DLBCL |Reddy cohort | 5.81 | |
| 15 | 18 | |DLBCL |Chapuy cohort |10.26 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EWSR1.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [EWSR1] |
|
| 1 | +# EWSR1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|------------------------| |
| 7 | 7 | |MCL |1 |high-confidence MCL gene| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:-------------:|:-------------:| |
| 12 | 13 | |MCL |GAMBL genomes|3.32 | |
| 13 | 14 | |
| 14 | -## Mutation pattern |
|
| 15 | +## Mutation pattern and selective pressure estimates |
|
| 15 | 16 | |
| 16 | 17 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 17 | 18 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EXOSC6.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EXOSC6] |
|
| 1 | +# EXOSC6 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EZH2.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [EZH2] |
|
| 1 | +# EZH2 |
|
| 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 | 5.56 | |
| 21 | 22 | |FL |GAMBL genomes |24.94 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
EZR.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [EZR] |
|
| 1 | +# EZR |
|
| 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 |1.70 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FAM102A.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FAM102A] |
|
| 1 | +# FAM102A |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |2.90 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FAM129B.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FAM129B] |
|
| 1 | +# FAM129B |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FAM38B.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FAM38B] |
|
| 1 | +# FAM38B |
|
| 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 |
FANK1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FANK1] |
|
| 1 | +# FANK1 |
|
| 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 |1.00 | |
| 15 | 16 | |DLBCL |Chapuy cohort |0.85 | |
| 16 | 17 | |
| 17 | -## Mutation pattern |
|
| 18 | +## Mutation pattern and selective pressure estimates |
|
| 18 | 19 | |
| 19 | 20 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 20 | 21 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FAS.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [FAS] |
|
| 1 | +# FAS |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------------------| |
| 7 | 7 | |BL |2 |relevance in BL not firmly established| |
| 8 | 8 | |DLBCL |1 |high-confidence DLBCL gene | |
| 9 | 9 | |FL |1 |high-confidence FL gene | |
| 10 | -## Mutation incidence |
|
| 10 | + |
|
| 11 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 11 | 12 | |
| 12 | 13 | |Entity|source |frequency (%)| |
| 13 | 14 | |:------:|:---------------------:|:-------------:| |
| ... | ... | @@ -20,7 +21,7 @@ |
| 20 | 21 | |DLBCL |Chapuy cohort | 8.97 | |
| 21 | 22 | |FL |GAMBL genomes | 5.08 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FAT4.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [FAT4] |
|
| 1 | +# FAT4 |
|
| 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 |2 |relevance in MCL not firmly established | |
| 9 | -## Mutation incidence |
|
| 9 | + |
|
| 10 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 10 | 11 | |
| 11 | 12 | |Entity|source |frequency (%)| |
| 12 | 13 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -16,7 +17,7 @@ |
| 16 | 17 | |DLBCL |Chapuy cohort |16.67 | |
| 17 | 18 | |MCL |GAMBL genomes | 3.79 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FBXO11.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [FBXO11] |
|
| 1 | +# FBXO11 |
|
| 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 | 2.10 | |
| 19 | 20 | |DLBCL |Chapuy cohort | 2.56 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FBXW7.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FBXW7] |
|
| 1 | +# FBXW7 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FCRL3.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FCRL3] |
|
| 1 | +# FCRL3 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |2.70 | |
| 15 | 16 | |DLBCL |Chapuy cohort |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FGFR3.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FGFR3] |
|
| 1 | +# FGFR3 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FIP1L1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FIP1L1] |
|
| 1 | +# FIP1L1 |
|
| 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 |2.50 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FLYWCH1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FLYWCH1] |
|
| 1 | +# FLYWCH1 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FNBP1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FNBP1] |
|
| 1 | +# FNBP1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |1.30 | |
| 15 | 16 | |DLBCL |Chapuy cohort |0.85 | |
| 16 | 17 | |
| 17 | -## Mutation pattern |
|
| 18 | +## Mutation pattern and selective pressure estimates |
|
| 18 | 19 | |
| 19 | 20 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 20 | 21 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |