22852567ed1ad3762fcc23112619e482c727a8b5
FNDC1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FNDC1] |
|
| 1 | +# FNDC1 |
|
| 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 |2.56 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FOXC1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FOXC1] |
|
| 1 | +# FOXC1 |
|
| 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 |1.20 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FOXO1.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [FOXO1] |
|
| 1 | +# FOXO1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------| |
| 7 | 7 | |BL |1 |high-confidence BL gene | |
| 8 | 8 | |DLBCL |1 |high-confidence DLBCL gene| |
| 9 | 9 | |FL |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 | 2.14 | |
| 21 | 22 | |FL |GAMBL genomes |12.93 | |
| 22 | 23 | |
| 23 | -## Mutation pattern |
|
| 24 | +## Mutation pattern and selective pressure estimates |
|
| 24 | 25 | |
| 25 | 26 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 26 | 27 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FOXP1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FOXP1] |
|
| 1 | +# FOXP1 |
|
| 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 |2.10 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FTCD.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FTCD] |
|
| 1 | +# FTCD |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FUBP1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FUBP1] |
|
| 1 | +# FUBP1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |1.50 | |
| 15 | 16 | |DLBCL |Chapuy cohort |0.85 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FUT5.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FUT5] |
|
| 1 | +# FUT5 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |0.30 | |
| 15 | 16 | |DLBCL |Chapuy cohort |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FZD3.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [FZD3] |
|
| 1 | +# FZD3 |
|
| 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 |1.00 | |
| 15 | 16 | |
| 16 | -## Mutation pattern |
|
| 17 | +## Mutation pattern and selective pressure estimates |
|
| 17 | 18 | |
| 18 | 19 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 19 | 20 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
FZR1.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [FZR1] |
|
| 1 | +# FZR1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------------------| |
| 7 | 7 | |FL |2 |relevance in FL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:-------------:|:-------------:| |
| 12 | 13 | |FL |GAMBL genomes|1.15 | |
| 13 | 14 | |
| 14 | -## Mutation pattern |
|
| 15 | +## Mutation pattern and selective pressure estimates |
|
| 15 | 16 | |
| 16 | 17 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 17 | 18 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GABRA2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GABRA2] |
|
| 1 | +# GABRA2 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GAK.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GAK] |
|
| 1 | +# GAK |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GBP7.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [GBP7] |
|
| 1 | +# GBP7 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GGTLA4.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GGTLA4] |
|
| 1 | +# GGTLA4 |
|
| 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 |
GNA13.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [GNA13] |
|
| 1 | +# GNA13 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------| |
| 7 | 7 | |BL |1 |high-confidence BL gene | |
| 8 | 8 | |DLBCL |1 |high-confidence DLBCL gene| |
| 9 | 9 | |FL |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 |10.26 | |
| 21 | 22 | |FL |GAMBL genomes |10.16 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GNAI2.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [GNAI2] |
|
| 1 | +# GNAI2 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------| |
| 7 | 7 | |BL |1 |high-confidence BL gene | |
| 8 | 8 | |DLBCL |1 |high-confidence DLBCL gene| |
| 9 | 9 | |FL |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 | 3.85 | |
| 21 | 22 | |FL |GAMBL genomes | 4.16 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GNAS.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GNAS] |
|
| 1 | +# GNAS |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GOLGA5.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GOLGA5] |
|
| 1 | +# GOLGA5 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GPC5.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GPC5] |
|
| 1 | +# GPC5 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |2.20 | |
| 15 | 16 | |DLBCL |Chapuy cohort |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GRB2.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [GRB2] |
|
| 1 | +# GRB2 |
|
| 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 |1.50 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GRHPR.md
| ... | ... | @@ -1,11 +1,14 @@ |
| 1 | +# GRHPR |
|
| 2 | +## Overview |
|
| 1 | 3 | GRHPR 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 @@ GRHPR is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 14 | 17 | |DLBCL |Reddy cohort |3.60 | |
| 15 | 18 | |DLBCL |Chapuy cohort |4.70 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GRIK5.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GRIK5] |
|
| 1 | +# GRIK5 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GRIN2A.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [GRIN2A] |
|
| 1 | +# GRIN2A |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GRM6.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [GRM6] |
|
| 1 | +# GRM6 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GSG2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GSG2] |
|
| 1 | +# GSG2 |
|
| 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 |2.14 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
GTSE1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [GTSE1] |
|
| 1 | +# GTSE1 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HDAC7.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HDAC7] |
|
| 1 | +# HDAC7 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HEPH.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [HEPH] |
|
| 1 | +# HEPH |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H1B.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HIST1H1B] |
|
| 1 | +# HIST1H1B |
|
| 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 |9.83 | |
| 21 | 22 | |FL |GAMBL genomes |5.54 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H1C.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HIST1H1C] |
|
| 1 | +# HIST1H1C |
|
| 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 | 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H1D.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HIST1H1D] |
|
| 1 | +# HIST1H1D |
|
| 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 |7.69 | |
| 21 | 22 | |FL |GAMBL genomes |3.23 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H1E.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HIST1H1E] |
|
| 1 | +# HIST1H1E |
|
| 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 |11.54 | |
| 21 | 22 | |FL |GAMBL genomes |12.93 | |
| 22 | 23 | |
| 23 | -## Mutation pattern |
|
| 24 | +## Mutation pattern and selective pressure estimates |
|
| 24 | 25 | |
| 25 | 26 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 26 | 27 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2AC.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HIST1H2AC] |
|
| 1 | +# HIST1H2AC |
|
| 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 |2.31 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2AG.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HIST1H2AG] |
|
| 1 | +# HIST1H2AG |
|
| 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 | 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 |2.99 | |
| 21 | 22 | |FL |GAMBL genomes |2.08 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2AM.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HIST1H2AM] |
|
| 1 | +# HIST1H2AM |
|
| 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 |5.98 | |
| 21 | 22 | |FL |GAMBL genomes |3.70 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2BC.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HIST1H2BC] |
|
| 1 | +# HIST1H2BC |
|
| 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 |3.46 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2BD.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [HIST1H2BD] |
|
| 1 | +# HIST1H2BD |
|
| 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|1.15 | |
| 13 | 14 | |
| 14 | -## Mutation pattern |
|
| 15 | +## Mutation pattern and selective pressure estimates |
|
| 15 | 16 | |
| 16 | 17 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 17 | 18 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2BG.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [HIST1H2BG] |
|
| 1 | +# HIST1H2BG |
|
| 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|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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2BK.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HIST1H2BK] |
|
| 1 | +# HIST1H2BK |
|
| 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 |4.20 | |
| 19 | 20 | |DLBCL |Chapuy cohort |5.56 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H2BM.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [HIST1H2BM] |
|
| 1 | +# HIST1H2BM |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H3B.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HIST1H3B] |
|
| 1 | +# HIST1H3B |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H3D.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HIST1H3D] |
|
| 1 | +# HIST1H3D |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H3G.md
| ... | ... | @@ -1,17 +1,18 @@ |
| 1 | -# [HIST1H3G] |
|
| 1 | +# HIST1H3G |
|
| 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|1.62 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H3H.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HIST1H3H] |
|
| 1 | +# HIST1H3H |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------------------| |
| 7 | 7 | |BL |2 |relevance in BL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:---------------------:|:-------------:| |
| ... | ... | @@ -13,7 +14,7 @@ |
| 13 | 14 | |BL |Thomas cohort |1.30 | |
| 14 | 15 | |BL |Panea cohort |5.90 | |
| 15 | 16 | |
| 16 | -## Mutation pattern |
|
| 17 | +## Mutation pattern and selective pressure estimates |
|
| 17 | 18 | |
| 18 | 19 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 19 | 20 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H3I.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HIST1H3I] |
|
| 1 | +# HIST1H3I |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------------------| |
| 7 | 7 | |BL |2 |relevance in BL not firmly established| |
| 8 | 8 | |FL |2 |relevance in FL not firmly established| |
| 9 | -## Mutation incidence |
|
| 9 | + |
|
| 10 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 10 | 11 | |
| 11 | 12 | |Entity|source |frequency (%)| |
| 12 | 13 | |:------:|:---------------------:|:-------------:| |
| ... | ... | @@ -15,7 +16,7 @@ |
| 15 | 16 | |BL |Panea cohort |2.00 | |
| 16 | 17 | |FL |GAMBL genomes |1.15 | |
| 17 | 18 | |
| 18 | -## Mutation pattern |
|
| 19 | +## Mutation pattern and selective pressure estimates |
|
| 19 | 20 | |
| 20 | 21 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 21 | 22 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H3J.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HIST1H3J] |
|
| 1 | +# HIST1H3J |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST1H4J.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HIST1H4J] |
|
| 1 | +# HIST1H4J |
|
| 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 | 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HIST2H2BE.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HIST2H2BE] |
|
| 1 | +# HIST2H2BE |
|
| 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 |2.60 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-A.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HLA-A] |
|
| 1 | +# HLA-A |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------------------| |
| 7 | 7 | |BL |2 |relevance in BL not firmly established| |
| 8 | 8 | |DLBCL |1 |high-confidence DLBCL gene | |
| 9 | -## Mutation incidence |
|
| 9 | + |
|
| 10 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 10 | 11 | |
| 11 | 12 | |Entity|source |frequency (%)| |
| 12 | 13 | |:------:|:---------------------:|:-------------:| |
| ... | ... | @@ -18,7 +19,7 @@ |
| 18 | 19 | |DLBCL |Reddy cohort | 0.20 | |
| 19 | 20 | |DLBCL |Chapuy cohort | 8.97 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-B.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HLA-B] |
|
| 1 | +# HLA-B |
|
| 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 |10.68 | |
| 21 | 22 | |FL |GAMBL genomes | 3.46 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-C.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HLA-C] |
|
| 1 | +# HLA-C |
|
| 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 | NA | |
| 15 | 16 | |DLBCL |Chapuy cohort |4.70 | |
| 16 | 17 | |
| 17 | -## Mutation pattern |
|
| 18 | +## Mutation pattern and selective pressure estimates |
|
| 18 | 19 | |
| 19 | 20 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 20 | 21 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-DMA.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HLA-DMA] |
|
| 1 | +# HLA-DMA |
|
| 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 | NA | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-DMB.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HLA-DMB] |
|
| 1 | +# HLA-DMB |
|
| 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 | NA | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-DQA1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HLA-DQA1] |
|
| 1 | +# HLA-DQA1 |
|
| 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 |0.30 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HLA-DQB1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HLA-DQB1] |
|
| 1 | +# HLA-DQB1 |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HNF1B.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HNF1B] |
|
| 1 | +# HNF1B |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |0.30 | |
| 15 | 16 | |DLBCL |Chapuy cohort |0.85 | |
| 16 | 17 | |
| 17 | -## Mutation pattern |
|
| 18 | +## Mutation pattern and selective pressure estimates |
|
| 18 | 19 | |
| 19 | 20 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 20 | 21 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HNRNPD.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HNRNPD] |
|
| 1 | +# HNRNPD |
|
| 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 |0.85 | |
| 17 | 18 | |FL |GAMBL genomes | NA | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HNRNPH1.md
| ... | ... | @@ -1,12 +1,13 @@ |
| 1 | -# [HNRNPH1] |
|
| 1 | +# HNRNPH1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|--------------------------| |
| 7 | 7 | |DLBCL |1 |high-confidence DLBCL gene| |
| 8 | 8 | |MCL |1 |high-confidence MCL gene | |
| 9 | -## Mutation incidence |
|
| 9 | + |
|
| 10 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 10 | 11 | |
| 11 | 12 | |Entity|source |frequency (%)| |
| 12 | 13 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -16,7 +17,7 @@ |
| 16 | 17 | |DLBCL |Chapuy cohort |3.42 | |
| 17 | 18 | |MCL |GAMBL genomes |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HNRNPU.md
| ... | ... | @@ -1,12 +1,15 @@ |
| 1 | +# HNRNPU |
|
| 2 | +## Overview |
|
| 1 | 3 | HNRNPU is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 2 | 4 | |
| 3 | -## Mutation tier |
|
| 5 | +## Relevance tier by entity |
|
| 4 | 6 | |
| 5 | 7 | |Entity|Tier|Description | |
| 6 | 8 | |:------:|:----:|--------------------------| |
| 7 | 9 | |BL |1-a | aSHM target and high-confidence BL gene | |
| 8 | 10 | |DLBCL |1-a | aSHM target and high-confidence DLBCL gene| |
| 9 | -## 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 @@ HNRNPU is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm |
| 18 | 21 | |DLBCL |Reddy cohort |2.40 | |
| 19 | 22 | |DLBCL |Chapuy cohort |3.42 | |
| 20 | 23 | |
| 21 | -## Mutation pattern |
|
| 24 | +## Mutation pattern and selective pressure estimates |
|
| 22 | 25 | |
| 23 | 26 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 24 | 27 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HNRNPU.pdf
| ... | ... | Binary files /dev/null and b/HNRNPU.pdf differ |
HRAS.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [HRAS] |
|
| 1 | +# HRAS |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
HVCN1.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [HVCN1] |
|
| 1 | +# HVCN1 |
|
| 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 |3.42 | |
| 21 | 22 | |FL |GAMBL genomes |6.47 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ICK.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [ICK] |
|
| 1 | +# ICK |
|
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
ID3.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [ID3] |
|
| 1 | +# ID3 |
|
| 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 |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
| 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 | 0.85 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IER2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IER2] |
|
| 1 | +# IER2 |
|
| 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 |0.60 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IFNGR1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IFNGR1] |
|
| 1 | +# IFNGR1 |
|
| 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 | 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IGLL5.md
| ... | ... | @@ -1,13 +1,14 @@ |
| 1 | -# [IGLL5] |
|
| 1 | +# IGLL5 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous | |
| 8 | 8 | |DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
| 9 | 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 | 8.97 | |
| 21 | 22 | |FL |GAMBL genomes |35.33 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IKBKB.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IKBKB] |
|
| 1 | +# IKBKB |
|
| 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 |3.42 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IKBKE.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IKBKE] |
|
| 1 | +# IKBKE |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2 |relevance in DLBCL not firmly established| |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |1.00 | |
| 15 | 16 | |DLBCL |Chapuy cohort |2.14 | |
| 16 | 17 | |
| 17 | -## Mutation pattern |
|
| 18 | +## Mutation pattern and selective pressure estimates |
|
| 18 | 19 | |
| 19 | 20 | |Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
| 20 | 21 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IKZF3.md
| ... | ... | @@ -1,12 +1,15 @@ |
| 1 | +# IKZF3 |
|
| 2 | +## Overview |
|
| 1 | 3 | IKZF3 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 @@ IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 18 | 21 | |DLBCL |Reddy cohort |3.90 | |
| 19 | 22 | |DLBCL |Chapuy cohort |4.27 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IL16.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IL16] |
|
| 1 | +# IL16 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IL4R.md
| ... | ... | @@ -1,11 +1,14 @@ |
| 1 | +# IL4R |
|
| 2 | +## Overview |
|
| 1 | 3 | IL4R 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 @@ IL4R is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 14 | 17 | |DLBCL |Reddy cohort |2.50 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IL6.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IL6] |
|
| 1 | +# IL6 |
|
| 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 |1.71 | |
| 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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
INO80.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [INO80] |
|
| 1 | +# INO80 |
|
| 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 |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |
IRAG2.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IRAG2] |
|
| 1 | +# IRAG2 |
|
| 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 |
IRF1.md
| ... | ... | @@ -1,11 +1,12 @@ |
| 1 | -# [IRF1] |
|
| 1 | +# IRF1 |
|
| 2 | 2 | |
| 3 | -## Mutation tier |
|
| 3 | +## Relevance tier by entity |
|
| 4 | 4 | |
| 5 | 5 | |Entity|Tier|Description | |
| 6 | 6 | |:------:|:----:|-----------------------------------------| |
| 7 | 7 | |DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
| 8 | -## Mutation incidence |
|
| 8 | + |
|
| 9 | +## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 9 | 10 | |
| 10 | 11 | |Entity|source |frequency (%)| |
| 11 | 12 | |:------:|:--------------:|:-------------:| |
| ... | ... | @@ -14,7 +15,7 @@ |
| 14 | 15 | |DLBCL |Reddy cohort |1.90 | |
| 15 | 16 | |DLBCL |Chapuy cohort |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 | |:------:|:----:|:---------------------:|:----------------:|:----------------:| |