Audit-of-B\342\200\220cell-Cancer-Genes.md
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@@ -1,5 +1,3 @@
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This is a community-driven resource and knowledge base initiated by members of the Lymphoma/Leukemia Molecular Profiling Project and fuelled by results from the genomic analysis of mature B-cell lymphomas (GAMBL) project. ## ATR Expression
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![image](images/gene_expression/ATR_by_pathology.svg)
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-<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
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-<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CYP2A6.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|FL |2 |relevance in FL not firmly established|
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+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
35 35
## CYP2A6 Expression
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![image](images/gene_expression/CYP2A6_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
CYP4F22.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
## CYP4F22 Expression
38 38
![image](images/gene_expression/CYP4F22_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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+<!-- BL: loveGeneticLandscapeMutations2012 -->
DAZAP1.md
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@@ -6,8 +6,8 @@ This gene has some recurrent sites of mutations (hot spots). The mutation patter
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|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
10
-|MCL |1 |high-confidence MCL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
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+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
11 11
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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@@ -52,3 +52,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
52 52
## References
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1. *Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.*
54 54
<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
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+<!-- DLBCL: pararajalingamCodingNoncodingDrivers2020 -->
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+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
DCAF6.md
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1 1
# DCAF6
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+## History
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+Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
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## Relevance tier by entity
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
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@@ -37,4 +39,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
37 39
![image](images/proteinpaint/DCAF6.svg)
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## DCAF6 Expression
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![image](images/gene_expression/DCAF6_by_pathology.svg)
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+
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+## References
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+1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
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+
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+
40 47
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
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+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
DDX10.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
38 38
## DDX10 Expression
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![image](images/gene_expression/DDX10_by_pathology.svg)
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<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
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+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
DDX3X.md
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@@ -6,9 +6,9 @@ Mutations in the DDX3X gene, which encodes an RNA helicase involved in various a
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|BL |1 | high-confidence BL gene |
10
-|DLBCL |1 | high-confidence DLBCL gene |
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-|FL |2 | Although recurrent, the relevance of mutations in FL is tenuous |
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+|![BL](images/icons/BL_tier1.png) |1 | high-confidence BL gene |
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+|![DLBCL](images/icons/DLBCL_tier1.png) |1 | high-confidence DLBCL gene |
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+|![FL](images/icons/FL_tier2.png) |2 | Although recurrent, the relevance of mutations in FL is tenuous |
12 12
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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@@ -57,3 +57,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
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## DDX3X Expression
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![image](images/gene_expression/DDX3X_by_pathology.svg)
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<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
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+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
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+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
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+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
DHDH.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|---------------------------------------|
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-|MCL |2 |relevance in MCL not firmly established|
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+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
35 35
## DHDH Expression
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![image](images/gene_expression/DHDH_by_pathology.svg)
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<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
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+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
DHX15.md
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@@ -6,7 +6,7 @@ Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|FL |2 |relevance in FL not firmly established|
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+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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DHX16.md
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@@ -6,7 +6,7 @@ Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et a
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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DICER1.md
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
41 41
## DICER1 Expression
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![image](images/gene_expression/DICER1_by_pathology.svg)
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<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
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+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
DLC1.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|---------------------------------------|
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-|MCL |2 |relevance in MCL not firmly established|
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+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
35 35
## DLC1 Expression
36 36
![image](images/gene_expression/DLC1_by_pathology.svg)
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<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
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+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
DLGAP1.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
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-|BL |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
37 37
## DLGAP1 Expression
38 38
![image](images/gene_expression/DLGAP1_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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+<!-- BL: loveGeneticLandscapeMutations2012 -->
DNAH5.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
38 38
## DNAH5 Expression
39 39
![image](images/gene_expression/DNAH5_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
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+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
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+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
DNM2.md
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@@ -6,7 +6,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|-----------------------------------------|
9
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
DNMT1.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
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-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
37 37
## DNMT1 Expression
38 38
![image](images/gene_expression/DNMT1_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
DNMT3A.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
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-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
38 38
## DNMT3A Expression
39 39
![image](images/gene_expression/DNMT3A_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
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+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
DOCK1.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
38 38
## DOCK1 Expression
39 39
![image](images/gene_expression/DOCK1_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
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+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
DSG4.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
38 38
## DSG4 Expression
39 39
![image](images/gene_expression/DSG4_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
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+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
DTX1.md
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@@ -6,9 +6,9 @@ Mutations in the DTX1 gene, which encodes the E3 ubiquitin ligase Deltex 1, have
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7 7
|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
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-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
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-|FL |1-a | aSHM target and high-confidence FL gene |
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+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
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+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
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@@ -103,4 +103,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
103 103
## References
104 104
1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*
105 105
2. *de Miranda NF, Georgiou K, Chen L, Wu C, Gao Z, Zaravinos A, Lisboa S, Enblad G, Teixeira MR, Zeng Y, Peng R, Pan-Hammarström Q. Exome sequencing reveals novel mutation targets in diffuse large B-cell lymphomas derived from Chinese patients. Blood. 2014 Oct 16;124(16):2544-53. doi: 10.1182/blood-2013-12-546309. Epub 2014 Aug 29. PMID: 25171927; PMCID: PMC4199956.*
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-<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
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+<!-- ORIGIN: 29641966 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
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+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
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+<!-- MZL: rossiCodingGenomeSplenic2012c -->
DUSP2.md
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@@ -7,8 +7,8 @@ DUSP2 functions as a negative regulator of MAPK signaling, particularly affectin
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|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------------------|
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-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
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-|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
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+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
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+|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
12 12
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
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@@ -68,3 +68,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
68 68
## DUSP2 Expression
69 69
![image](images/gene_expression/DUSP2_by_pathology.svg)
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<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
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+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
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+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
E2F2.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|BL |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
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## E2F2 Expression
38 38
![image](images/gene_expression/E2F2_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
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+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
EBF1.md
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@@ -8,9 +8,9 @@ EBF1 is a critical transcription factor in early B-cell development, regulating
8 8
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|Entity|Tier|Description |
10 10
|:------:|:----:|--------------------------------------|
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-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
12
-|FL |1-a | aSHM target and high-confidence FL gene |
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-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
11
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
12
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
13
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
14 14
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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EDNRB.md
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@@ -4,7 +4,7 @@
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|BL |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## EDNRB Expression
38 38
![image](images/gene_expression/EDNRB_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
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+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
EEF1A1.md
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@@ -5,13 +5,12 @@ Mutations in the EEF1A1 gene, which encodes the eukaryotic translation elongatio
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## History
6 6
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
7 7
8
-
9 8
## Relevance tier by entity
10 9
11 10
|Entity|Tier|Description |
12 11
|:------:|:----:|--------------------------------------|
13
-|DLBCL |1 |high-confidence DLBCL gene |
14
-|FL |2 |relevance in FL not firmly established|
12
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
13
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
15 14
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
17 16
EHD1.md
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@@ -4,7 +4,7 @@
4 4
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|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
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@@ -34,3 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
34 34
## EHD1 Expression
35 35
![image](images/gene_expression/EHD1_by_pathology.svg)
36 36
<!-- ORIGIN: Unknown -->
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+<!-- BL: 2 -->
EIF2AK3.md
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@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,4 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
34 34
![image](images/proteinpaint/EIF2AK3.svg)
35 35
## EIF2AK3 Expression
36 36
![image](images/gene_expression/EIF2AK3_by_pathology.svg)
37
-<!-- ORIGIN: NA -->
37
+<!-- ORIGIN: Unknown -->
EIF2AK4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
35 35
## EIF2AK4 Expression
36 36
![image](images/gene_expression/EIF2AK4_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
EIF2C4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
31 31
## EIF2C4 Expression
32 32
![image](images/gene_expression/EIF2C4_by_pathology.svg)
33 33
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34
+<!-- BL: loveGeneticLandscapeMutations2012 -->
EIF4A1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|BL |1 |high-confidence BL gene|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## EIF4A1 Expression
38 38
![image](images/gene_expression/EIF4A1_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
EML2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## EML2 Expression
38 38
![image](images/gene_expression/EML2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
ENTPD3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## ENTPD3 Expression
38 38
![image](images/gene_expression/ENTPD3_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
EP300.md
... ...
@@ -6,9 +6,9 @@ Mutations in EP300 are significant contributors to the pathogenesis and progress
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|FL |1 |high-confidence FL gene |
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -84,4 +84,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
84 84
85 85
4. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
86 86
87
-<!-- ORIGIN: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
87
+<!-- ORIGIN: 21390126 -->
88
+<!-- FL: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
89
+<!-- BL: 2 -->
90
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
91
+<!-- DLBCL: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
EPHB2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## EPHB2 Expression
38 38
![image](images/gene_expression/EPHB2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
ERAP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## ERAP1 Expression
38 38
![image](images/gene_expression/ERAP1_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
ESX1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
35 35
## ESX1 Expression
36 36
![image](images/gene_expression/ESX1_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
ETS1.md
... ...
@@ -6,8 +6,8 @@ ETS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
10
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -75,3 +75,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
75 75
1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
76 76
77 77
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
78
+<!-- BL: paneaWholeGenomeLandscape2019 -->
79
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
ETV6.md
... ...
@@ -6,7 +6,7 @@ ETV6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -51,3 +51,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
51 51
## ETV6 Expression
52 52
![image](images/gene_expression/ETV6_by_pathology.svg)
53 53
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
54
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
EWSR1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
35 35
## EWSR1 Expression
36 36
![image](images/gene_expression/EWSR1_by_pathology.svg)
37 37
<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
38
+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
EXOSC6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
37 37
## EXOSC6 Expression
38 38
![image](images/gene_expression/EXOSC6_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
EZR.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
FAM102A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
FAM129B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
35 35
## FAM129B Expression
36 36
![image](images/gene_expression/FAM129B_by_pathology.svg)
37 37
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
38
+<!-- BL: loveGeneticLandscapeMutations2012 -->
FAM38B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -25,3 +25,4 @@
25 25
## FAM38B Expression
26 26
![image](images/gene_expression/FAM38B_by_pathology.svg)
27 27
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
28
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
FANK1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -39,4 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
39 39
![image](images/proteinpaint/FANK1.svg)
40 40
## FANK1 Expression
41 41
![image](images/gene_expression/FANK1_by_pathology.svg)
42
-<!-- ORIGIN: NA -->
42
+<!-- ORIGIN: Unknown -->
FAS.md
... ...
@@ -6,9 +6,8 @@ FAS encodes a cell surface receptor involved in the induction of apoptosis. FAS
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
11
-|BL |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
... ...
@@ -50,3 +49,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
50 49
## FAS Expression
51 50
![image](images/gene_expression/FAS_by_pathology.svg)
52 51
<!-- ORIGIN: schollMutationsRegionFAS2007 -->
52
+<!-- DLBCL: schollMutationsRegionFAS2007 -->
53
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
FAT4.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
8
-|MCL |2 |relevance in MCL not firmly established |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -40,3 +40,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
40 40
## FAT4 Expression
41 41
![image](images/gene_expression/FAT4_by_pathology.svg)
42 42
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
43
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
44
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
45
+<!-- MZL: parryWholeExomeSequencing2013 -->
FBXO11.md
... ...
@@ -9,8 +9,8 @@ Mutations in this gene were first described in BL in 2015 by Pighi et al<sup>4</
9 9
10 10
|Entity|Tier|Description |
11 11
|:------:|:----:|--------------------------|
12
-|BL |1 |high-confidence BL gene |
13
-|DLBCL |1 |high-confidence DLBCL gene|
12
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
14 14
15 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
16 16
FBXW7.md
... ...
@@ -6,7 +6,7 @@ FBXW7 mutations are found in a range of lymphoid malignancies, including B-cell
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
FCRL3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
FGFR3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
37 37
## FGFR3 Expression
38 38
![image](images/gene_expression/FGFR3_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
FLYWCH1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
37 37
## FLYWCH1 Expression
38 38
![image](images/gene_expression/FLYWCH1_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
FNBP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
FNDC1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
38 38
## FNDC1 Expression
39 39
![image](images/gene_expression/FNDC1_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
FOXC1.md
... ...
@@ -6,7 +6,7 @@ FOXC1 is a transcription factor that regulates genes involved in cell growth, di
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
FOXO1.md
... ...
@@ -6,9 +6,9 @@ Mutations in the FOXO1 gene, which encodes a member of the forkhead family of tr
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|BL |1 |high-confidence BL gene |
10
-|DLBCL |1 |high-confidence DLBCL gene|
11
-|FL |1 |high-confidence FL gene |
9
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
11
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
FTCD.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
37 37
## FTCD Expression
38 38
![image](images/gene_expression/FTCD_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
FUT5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
38 38
## FUT5 Expression
39 39
![image](images/gene_expression/FUT5_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
FZD3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
FZR1.md
... ...
@@ -6,7 +6,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|FL |2 |relevance in FL not firmly established|
9
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
GABRA2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
38 38
## GABRA2 Expression
39 39
![image](images/gene_expression/GABRA2_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
GAK.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et a
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|-----------------------------------------|
10
-|DLBCL |2 |relevance in DLBCL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
GBP7.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
35 35
## GBP7 Expression
36 36
![image](images/gene_expression/GBP7_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
GGTLA4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
31 31
## GGTLA4 Expression
32 32
![image](images/gene_expression/GGTLA4_by_pathology.svg)
33 33
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34
+<!-- BL: loveGeneticLandscapeMutations2012 -->
GNA13.md
... ...
@@ -6,9 +6,9 @@ Mutations in GNA13, which encodes a G protein alpha subunit involved in multiple
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|BL |1 |high-confidence BL gene |
10
-|DLBCL |1 |high-confidence DLBCL gene|
11
-|FL |1 |high-confidence FL gene |
9
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
11
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -63,3 +63,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
63 63
2. *Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM, Cyster JG. Loss of signalling via Gα13 in germinal centre B-cell-derived lymphoma. Nature. 2014 Dec 11;516(7530):254-8. doi: 10.1038/nature13765. Epub 2014 Sep 28. PMID: 25274307; PMCID: PMC4267955.*
64 64
3. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
65 65
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
66
+<!-- BL: loveGeneticLandscapeMutations2012 -->
67
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
68
+<!-- BL: loveGeneticLandscapeMutations2012 -->
69
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
GNAS.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
38 38
## GNAS Expression
39 39
![image](images/gene_expression/GNAS_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
GOLGA5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
38 38
## GOLGA5 Expression
39 39
![image](images/gene_expression/GOLGA5_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
GPC5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
38 38
## GPC5 Expression
39 39
![image](images/gene_expression/GPC5_by_pathology.svg)
40 40
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
GRB2.md
... ...
@@ -6,8 +6,8 @@ GRB2 (Growth factor receptor-bound protein 2) is an adaptor protein that links r
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|BL |2 |relevance in BL seems unlikely|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL seems unlikely|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -44,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
44 44
## GRB2 Expression
45 45
![image](images/gene_expression/GRB2_by_pathology.svg)
46 46
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
47
+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
48
+<!-- BL: paneaWholeGenomeLandscape2019 -->
GRHPR.md
... ...
@@ -7,7 +7,7 @@ GRHPR is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------|
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -49,3 +49,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
49 49
## GRHPR Expression
50 50
![image](images/gene_expression/GRHPR_by_pathology.svg)
51 51
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
52
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
GRIK5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
## GRIK5 Expression
38 38
![image](images/gene_expression/GRIK5_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
GRIN2A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
35 35
## GRIN2A Expression
36 36
![image](images/gene_expression/GRIN2A_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
GRM6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
35 35
## GRM6 Expression
36 36
![image](images/gene_expression/GRM6_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
GSG2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
38 38
## GSG2 Expression
39 39
![image](images/gene_expression/GSG2_by_pathology.svg)
40 40
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
GTSE1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
## GTSE1 Expression
38 38
![image](images/gene_expression/GTSE1_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
HDAC7.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
38 38
## HDAC7 Expression
39 39
![image](images/gene_expression/HDAC7_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
HEPH.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
35 35
## HEPH Expression
36 36
![image](images/gene_expression/HEPH_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
HIST1H1B.md
... ...
@@ -5,9 +5,9 @@ This is one of several genes that encode linker histone proteins that are recurr
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------------------|
8
-|BL |2 |relevance in BL not firmly established|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
8
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -42,3 +42,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
42 42
## HIST1H1B Expression
43 43
![image](images/gene_expression/HIST1H1B_by_pathology.svg)
44 44
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
45
+<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
46
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
47
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
HIST1H1D.md
... ...
@@ -5,9 +5,9 @@ This is one of several genes that encode linker histone proteins that are recurr
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------------------|
8
-|BL |2 |relevance in BL not firmly established|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
8
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -45,3 +45,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
45 45
## HIST1H1D Expression
46 46
![image](images/gene_expression/HIST1H1D_by_pathology.svg)
47 47
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
48
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
49
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
50
+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
HIST1H2AC.md
... ...
@@ -5,8 +5,8 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------|
8
-|DLBCL |1 |high-confidence DLBCL gene|
9
-|FL |1 |high-confidence FL gene |
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -63,3 +63,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
63 63
## HIST1H2AC Expression
64 64
![image](images/gene_expression/HIST1H2AC_by_pathology.svg)
65 65
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
66
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
67
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
HIST1H2AG.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
-|FL |1 |high-confidence FL gene |
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -52,4 +52,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
52 52
![image](images/proteinpaint/HIST1H2AG.svg)
53 53
## HIST1H2AG Expression
54 54
![image](images/gene_expression/HIST1H2AG_by_pathology.svg)
55
-<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
55
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
56
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
57
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
58
+<!-- BL: paneaWholeGenomeLandscape2019 -->
59
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
HIST1H2AM.md
... ...
@@ -5,9 +5,9 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------------------|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |1 |high-confidence FL gene |
10
-|BL |2 |relevance in BL not firmly established|
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -73,4 +73,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
73 73
![image](images/proteinpaint/HIST1H2AM.svg)
74 74
## HIST1H2AM Expression
75 75
![image](images/gene_expression/HIST1H2AM_by_pathology.svg)
76
-<!-- ORIGIN: NA -->
76
+<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
77
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
78
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST1H2BC.md
... ...
@@ -6,8 +6,8 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
10
-|FL |1 |high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -67,3 +67,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
67 67
## HIST1H2BC Expression
68 68
![image](images/gene_expression/HIST1H2BC_by_pathology.svg)
69 69
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
70
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
71
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
72
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
HIST1H2BD.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|FL |1 |high-confidence FL gene|
7
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -30,3 +30,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
30 30
## HIST1H2BD Expression
31 31
![image](images/gene_expression/HIST1H2BD_by_pathology.svg)
32 32
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
33
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
HIST1H2BG.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|FL |1 |high-confidence FL gene|
7
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -30,3 +30,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
30 30
## HIST1H2BG Expression
31 31
![image](images/gene_expression/HIST1H2BG_by_pathology.svg)
32 32
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
33
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
HIST1H2BK.md
... ...
@@ -6,8 +6,8 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -43,4 +43,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
43 43
![image](images/proteinpaint/HIST1H2BK.svg)
44 44
## HIST1H2BK Expression
45 45
![image](images/gene_expression/HIST1H2BK_by_pathology.svg)
46
-<!-- ORIGIN: NA -->
46
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
47
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
48
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST1H2BM.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
35 35
## HIST1H2BM Expression
36 36
![image](images/gene_expression/HIST1H2BM_by_pathology.svg)
37 37
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
38
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
HIST1H3B.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
8
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -48,3 +48,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
48 48
## HIST1H3B Expression
49 49
![image](images/gene_expression/HIST1H3B_by_pathology.svg)
50 50
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
51
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
52
+<!-- PMBL: reichelFlowSortingExome2015a -->
HIST1H3D.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
45 45
## HIST1H3D Expression
46 46
![image](images/gene_expression/HIST1H3D_by_pathology.svg)
47 47
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
48
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST1H3G.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|FL |1 |high-confidence FL gene|
7
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -32,3 +32,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
32 32
## HIST1H3G Expression
33 33
![image](images/gene_expression/HIST1H3G_by_pathology.svg)
34 34
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
35
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
HIST1H3H.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
37 37
## HIST1H3H Expression
38 38
![image](images/gene_expression/HIST1H3H_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST1H3I.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|FL |2 |relevance in FL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -39,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
39 39
## HIST1H3I Expression
40 40
![image](images/gene_expression/HIST1H3I_by_pathology.svg)
41 41
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
42
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
43
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST1H3J.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
45 45
## HIST1H3J Expression
46 46
![image](images/gene_expression/HIST1H3J_by_pathology.svg)
47 47
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
48
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST1H4J.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
37 37
## HIST1H4J Expression
38 38
![image](images/gene_expression/HIST1H4J_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
41
+<!-- BL: paneaWholeGenomeLandscape2019 -->
HIST2H2BE.md
... ...
@@ -6,7 +6,7 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
35 35
## HIST2H2BE Expression
36 36
![image](images/gene_expression/HIST2H2BE_by_pathology.svg)
37 37
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
38
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
HLA-A.md
... ...
@@ -6,8 +6,8 @@ Mutations in the HLA-B gene have been associated with a loss of cell surface exp
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -50,4 +50,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
50 50
1. *Riemersma, S., Jordanova, E., Schop, R., Philippo, K., Looijenga, L., Schuuring, E., & Kluin, P. (2000). Extensive genetic alterations of the HLA region, including homozygous deletions of HLA class II genes in B-cell lymphomas arising in immune-privileged sites.. Blood, 96 10, 3569-77 . https://doi.org/10.1182/BLOOD.V96.10.3569.*
51 51
## HLA-A Expression
52 52
![image](images/gene_expression/HLA-A_by_pathology.svg)
53
-<!-- ORIGIN: Unknown -->
53
+<!-- ORIGIN: deschGenotypingCirculatingTumor2020 -->
54
+<!-- BL: 2 -->
55
+<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
HLA-B.md
... ...
@@ -6,9 +6,9 @@ Mutations in the HLA-B gene have been associated with a loss of cell surface exp
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|FL |2 |relevance in FL not firmly established|
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -60,4 +60,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
60 60
## References
61 61
1. *Riemersma, S., Jordanova, E., Schop, R., Philippo, K., Looijenga, L., Schuuring, E., & Kluin, P. (2000). Extensive genetic alterations of the HLA region, including homozygous deletions of HLA class II genes in B-cell lymphomas arising in immune-privileged sites.. Blood, 96 10, 3569-77 . https://doi.org/10.1182/BLOOD.V96.10.3569.*
62 62
63
-<!-- ORIGIN: NA -->
63
+<!-- ORIGIN: wienandGenomicAnalysesFlowsorted2019b -->
64
+<!-- BL: 2 -->
65
+<!-- PMBL: wienandGenomicAnalysesFlowsorted2019b -->
HLA-C.md
... ...
@@ -6,7 +6,7 @@ Mutations in the HLA-C gene have been associated with a loss of cell surface exp
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -36,4 +36,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
36 36
![image](images/proteinpaint/HLA-C.svg)
37 37
## HLA-C Expression
38 38
![image](images/gene_expression/HLA-C_by_pathology.svg)
39
-<!-- ORIGIN: Unknown -->
39
+<!-- ORIGIN: gomezUltraDeepSequencingReveals2023 -->
40
+<!-- PMBL: gomezUltraDeepSequencingReveals2023 -->
HLA-DMA.md
... ...
@@ -6,7 +6,7 @@ Mutations in this gene are relatively rare in DLBCL overall. *Without further su
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
HLA-DMB.md
... ...
@@ -6,8 +6,8 @@ HLA-DMB, along with HLA-DMA, plays a critical role in the proper functioning of
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -40,5 +40,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
40 40
![image](images/proteinpaint/HLA-DMB.svg)
41 41
## HLA-DMB Expression
42 42
![image](images/gene_expression/HLA-DMB_by_pathology.svg)
43
-<!-- ORIGIN: Unknown -->
44
-<!-- BL: 2 -->
HLA-DQA1.md
... ...
@@ -10,7 +10,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
10 10
11 11
|Entity|Tier|Description |
12 12
|:------:|:----:|--------------------------|
13
-|DLBCL |1 |high-confidence DLBCL gene|
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
14 14
15 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
16 16
HLA-DQB1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
HNF1B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
38 38
## HNF1B Expression
39 39
![image](images/gene_expression/HNF1B_by_pathology.svg)
40 40
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
41
+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
HNRNPD.md
... ...
@@ -6,8 +6,8 @@ hnRNPs are a family of RNA-binding proteins that play crucial roles in RNA proce
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |2 |relevance in FL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
HNRNPH1.md
... ...
@@ -6,8 +6,8 @@ Non-coding mutations, including synonymous and intronic mutations, are enriched
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
10
-|MCL |1 |high-confidence MCL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -51,3 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
51 51
52 52
<!-- NONCODING -->
53 53
<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
54
+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
55
+<!-- DLBCL: pararajalingamCodingNoncodingDrivers2020 -->
HRAS.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
38 38
## HRAS Expression
39 39
![image](images/gene_expression/HRAS_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
42
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
HVCN1.md
... ...
@@ -6,9 +6,8 @@ HVCN1, a voltage-gated proton channel, has been identified as recurrently mutate
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
11
-|BL |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
... ...
@@ -54,4 +53,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
54 53
1. *Krysiak, K., Gomez, F., White, B., Matlock, M., Miller, C., Trani, L., Fronick, C., Fulton, R., Kreisel, F., Cashen, A., Carson, K., Berrien-Elliott, M., Bartlett, N., Griffith, M., Griffith, O., & Fehniger, T. (2017). Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma.. Blood, 129 4, 473-483 . https://doi.org/10.1182/blood-2016-07-729954.*
55 54
## HVCN1 Expression
56 55
![image](images/gene_expression/HVCN1_by_pathology.svg)
57
-<!-- ORIGIN: NA -->
56
+<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
57
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
ICK.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
35 35
## ICK Expression
36 36
![image](images/gene_expression/ICK_by_pathology.svg)
37 37
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
38
+<!-- BL: loveGeneticLandscapeMutations2012 -->
IER2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -29,3 +29,4 @@
29 29
## IER2 Expression
30 30
![image](images/gene_expression/IER2_by_pathology.svg)
31 31
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
32
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
IFNGR1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
38 38
## IFNGR1 Expression
39 39
![image](images/gene_expression/IFNGR1_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
IGLL5.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9
-|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
7
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9
+|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -48,4 +48,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
48 48
![image](images/proteinpaint/IGLL5.svg)
49 49
## IGLL5 Expression
50 50
![image](images/gene_expression/IGLL5_by_pathology.svg)
51
-<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
51
+<!-- ORIGIN: deschGenotypingCirculatingTumor2020 -->
52
+<!-- BL: paneaWholeGenomeLandscape2019 -->
53
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
54
+<!-- BL: paneaWholeGenomeLandscape2019 -->
IKBKE.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|-----------------------------------------|
10
-|DLBCL |2 |relevance in DLBCL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
IKZF3.md
... ...
@@ -6,8 +6,8 @@ IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription fac
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -74,3 +74,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
74 74
## IKZF3 Expression
75 75
![image](images/gene_expression/IKZF3_by_pathology.svg)
76 76
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
77
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
78
+<!-- BL: paneaWholeGenomeLandscape2019 -->
IL16.md
... ...
@@ -6,7 +6,7 @@ The IL16 gene, which encodes a pro-inflammatory cytokine, plays a role in immune
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -40,4 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
40 40
41 41
<!-- FLAGGED FOR TIER 2 -->
42 42
43
-<!-- ORIGIN: NA -->
43
+<!-- ORIGIN: Unknown -->
IL4R.md
... ...
@@ -6,7 +6,7 @@ Mutations in IL4R have been identified in various types of B-cell lymphomas, par
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -54,4 +54,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
54 54
2. *Viganò E, Gunawardana J, Mottok A, Van Tol T, Mak K, Chan FC, Chong L, Chavez E, Woolcock B, Takata K, Twa D, Shulha HP, Telenius A, Kutovaya O, Hung SS, Healy S, Ben-Neriah S, Leroy K, Gaulard P, Diepstra A, Kridel R, Savage KJ, Rimsza L, Gascoyne R, Steidl C. Somatic IL4R mutations in primary mediastinal large B-cell lymphoma lead to constitutive JAK-STAT signaling activation. Blood. 2018 May 3;131(18):2036-2046. doi: 10.1182/blood-2017-09-808907. Epub 2018 Feb 21. PMID: 29467182.*
55 55
## IL4R Expression
56 56
![image](images/gene_expression/IL4R_by_pathology.svg)
57
-<!-- ORIGIN: dunsCharacterizationDLBCLPMBL2021b -->
57
+<!-- ORIGIN: viganoSomaticIL4RMutations2018b -->
58
+<!-- DLBCL: dunsCharacterizationDLBCLPMBL2021b -->
59
+<!-- PMBL: viganoSomaticIL4RMutations2018b -->
IL6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
38 38
## IL6 Expression
39 39
![image](images/gene_expression/IL6_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
INO80.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
38 38
## INO80 Expression
39 39
![image](images/gene_expression/INO80_by_pathology.svg)
40 40
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
IRAG2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
IRF1.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|-----------------------------------------|
10
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
IRF4.md
... ...
@@ -6,8 +6,8 @@ IRF4 (Interferon Regulatory Factor 4) encodes a transcription factor that plays
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
10
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -61,3 +61,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
61 61
1. *Hans CP, Weisenburger DD, Greiner TC, Gascoyne RD, Delabie J, Ott G, Müller-Hermelink HK, Campo E, Braziel RM, Jaffe ES, Pan Z, Farinha P, Smith LM, Falini B, Banham AH, Rosenwald A, Staudt LM, Connors JM, Armitage JO, Chan WC. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray. Blood. 2004 Jan 1;103(1):275-82. doi: 10.1182/blood-2003-05-1545. Epub 2003 Sep 22. PMID: 14504078.*
62 62
2. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
63 63
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
64
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
65
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
IRF8.md
... ...
@@ -6,9 +6,9 @@ IRF8 (Interferon Regulatory Factor 8) is a transcription factor critical for the
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -69,3 +69,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
69 69
## IRF8 Expression
70 70
![image](images/gene_expression/IRF8_by_pathology.svg)
71 71
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
72
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
73
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
74
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
ITPKB.md
... ...
@@ -6,8 +6,8 @@ The ITPKB gene encodes inositol-trisphosphate 3-kinase B, an enzyme involved in
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
10
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -55,4 +55,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
55 55
1. *Mareschal S, Dubois S, Viailly PJ, Bertrand P, Bohers E, Maingonnat C, Jaïs JP, Tesson B, Ruminy P, Peyrouze P, Copie-Bergman C, Fest T, Jo Molina T, Haioun C, Salles G, Tilly H, Lecroq T, Leroy K, Jardin F. Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma. Genes Chromosomes Cancer. 2016 Mar;55(3):251-67. doi: 10.1002/gcc.22328. Epub 2015 Nov 26. PMID: 26608593.*
56 56
## ITPKB Expression
57 57
![image](images/gene_expression/ITPKB_by_pathology.svg)
58
-<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
58
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
59
+<!-- PMBL: reichelFlowSortingExome2015a -->
60
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
ITPR3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
## ITPR3 Expression
38 38
![image](images/gene_expression/ITPR3_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
41
+<!-- BL: loveGeneticLandscapeMutations2012 -->
JAK1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -44,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/J
44 44
## JAK1 Expression
45 45
![image](images/gene_expression/JAK1_by_pathology.svg)
46 46
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
47
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
48
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
JAK3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/J
38 38
## JAK3 Expression
39 39
![image](images/gene_expression/JAK3_by_pathology.svg)
40 40
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
JUNB.md
... ...
@@ -6,7 +6,7 @@ JUNB has been reported to be frequently mutated in T-cell/histiocyte-rich large
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -50,3 +50,5 @@ bioRxiv 2023.11.21.567983; doi: https://doi.org/10.1101/2023.11.21.567983*
50 50
## JUNB Expression
51 51
![image](images/gene_expression/JUNB_by_pathology.svg)
52 52
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
53
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
54
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
JUP.md
... ...
@@ -6,7 +6,7 @@ Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|FL |2 |relevance in FL not firmly established|
9
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
KCMF1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
38 38
## KCMF1 Expression
39 39
![image](images/gene_expression/KCMF1_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
KCNK10.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
37 37
## KCNK10 Expression
38 38
![image](images/gene_expression/KCNK10_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
KIFC3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
37 37
## KIFC3 Expression
38 38
![image](images/gene_expression/KIFC3_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
KIR3DL1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
35 35
## KIR3DL1 Expression
36 36
![image](images/gene_expression/KIR3DL1_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
KLF2.md
... ...
@@ -6,8 +6,8 @@ KLF2 (Kruppel-like factor 2) is a transcription factor involved in the regulatio
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
10
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
KLHL14.md
... ...
@@ -6,7 +6,7 @@ KLHL14 (Kelch-like family member 14) is a gene that has been identified as playi
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -54,3 +54,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
54 54
## KLHL14 Expression
55 55
![image](images/gene_expression/KLHL14_by_pathology.svg)
56 56
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
57
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
KLHL21.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
KLHL26.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
37 37
## KLHL26 Expression
38 38
![image](images/gene_expression/KLHL26_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
KLHL6.md
... ...
@@ -7,9 +7,9 @@ KLHL6 is considered a tumor suppressor gene in DLBCL with mutations tending to d
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------------------|
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |1-a | aSHM target and high-confidence FL gene |
12
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
12
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
13 13
14 14
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
15 15
... ...
@@ -80,3 +80,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
80 80
## References
81 81
1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
82 82
2. *Choi, J., Zhou, N., & Busino, L. (2019). KLHL6 is a tumor suppressor gene in diffuse large B-cell lymphoma. Cell Cycle, 18, 249 - 256. https://doi.org/10.1080/15384101.2019.1568765.*
83
+<!-- MZL: ganapathiGeneticLandscapeDural2016 -->
84
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
85
+<!-- BL: 2 -->
86
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
KMT2C.md
... ...
@@ -6,9 +6,9 @@ This gene has been reported to be recurrently mutated in DLBCL. The rate of muta
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|---------------------------------------|
9
-|BL |2 |relevance in BL not firmly established |
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|MCL |2 |relevance in MCL not firmly established|
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -53,3 +53,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
53 53
## KMT2C Expression
54 54
![image](images/gene_expression/KMT2C_by_pathology.svg)
55 55
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
56
+<!-- BL: zhouSporadicEndemicBurkitt2019 -->
57
+<!-- BL: zhouSporadicEndemicBurkitt2019 -->
58
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
59
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
KRAS.md
... ...
@@ -6,7 +6,7 @@ KRAS mutations are rare but occur in some cases of DLBCL.<sup>1</sup> These ofte
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
LAMA5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
38 38
## LAMA5 Expression
39 39
![image](images/gene_expression/LAMA5_by_pathology.svg)
40 40
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
LAPTM5.md
... ...
@@ -6,8 +6,8 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|-----------------------------------------|
9
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
10
-|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
10
+|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
LCOR.md
... ...
@@ -6,8 +6,8 @@ LCOR (Ligand Dependent Nuclear Receptor Corepressor) is involved in the regulati
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|BL |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
11 11
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -41,4 +41,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
41 41
![image](images/proteinpaint/LCOR_hg38.svg)
42 42
## LCOR Expression
43 43
![image](images/gene_expression/LCOR_by_pathology.svg)
44
-<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
44
+<!-- ORIGIN: 30275490 -->
45
+<!-- BL: 2 -->
46
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
LIN54.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
38 38
## LIN54 Expression
39 39
![image](images/gene_expression/LIN54_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
LPP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -51,3 +51,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
51 51
## LPP Expression
52 52
![image](images/gene_expression/LPP_by_pathology.svg)
53 53
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
54
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
LRP12.md
... ...
@@ -1,10 +1,12 @@
1 1
# LRP12
2
+## History
3
+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 10
9 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
... ...
@@ -37,4 +39,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
37 39
![image](images/proteinpaint/LRP12.svg)
38 40
## LRP12 Expression
39 41
![image](images/gene_expression/LRP12_by_pathology.svg)
42
+## References
43
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
44
+
45
+
40 46
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
47
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
LRRN3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
38 38
## LRRN3 Expression
39 39
![image](images/gene_expression/LRRN3_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
42
+<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
LTB.md
... ...
@@ -6,9 +6,9 @@ LTB (Lymphotoxin Beta) is a member of the tumor necrosis factor (TNF) superfamil
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10
-|FL |1-a | aSHM target and high-confidence FL gene |
11
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
11
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -51,4 +51,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
51 51
![image](images/gene_expression/LTB_by_pathology.svg)
52 52
53 53
## References
54
-<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
54
+<!-- ORIGIN: 29713087 -->
55
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
56
+<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
57
+<!-- BL: 2 -->
LYN.md
... ...
@@ -6,7 +6,7 @@ LYN mutations have been reported in DLBCL but the rate is relatively rare in mos
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
39 39
40 40
<!-- FLAGGED FOR TIER 2 -->
41 41
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
42
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
MAGEC1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
44 44
## MAGEC1 Expression
45 45
![image](images/gene_expression/MAGEC1_by_pathology.svg)
46 46
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
47
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
MAGT1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MAGT1 Expression
39 39
![image](images/gene_expression/MAGT1_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MALAT1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -36,3 +36,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
36 36
## MALAT1 Expression
37 37
![image](images/gene_expression/MALAT1_by_pathology.svg)
38 38
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
39
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
MAP2K1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
8
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -46,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
46 46
## MAP2K1 Expression
47 47
![image](images/gene_expression/MAP2K1_by_pathology.svg)
48 48
<!-- ORIGIN: shinBRAFV600EMAP2K12015 -->
49
+<!-- DLBCL: shinBRAFV600EMAP2K12015 -->
50
+<!-- FL: louissaintPediatrictypeNodalFollicular2016a -->
MAP3K6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
## MAP3K6 Expression
38 38
![image](images/gene_expression/MAP3K6_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
MAP4K4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MAP4K4 Expression
39 39
![image](images/gene_expression/MAP4K4_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MAP7D1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
35 35
## MAP7D1 Expression
36 36
![image](images/gene_expression/MAP7D1_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
MARK1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MARK1 Expression
39 39
![image](images/gene_expression/MARK1_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MCL1.md
... ...
@@ -6,8 +6,8 @@ MCL1 (Myeloid Cell Leukemia 1) is a member of the BCL2 family of proteins that p
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -54,3 +54,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
54 54
1. *Wenzel, S., Grau, M., Mavis, C., Hailfinger, S., Wolf, A., Madle, H., Deeb, G., Dörken, B., Thome, M., Lenz, P., Dirnhofer, S., Hernandez-Ilizaliturri, F., Tzankov, A., & Lenz, G. (2013). MCL1 is deregulated in subgroups of diffuse large B-cell lymphoma. Leukemia, 27, 1381-1390. https://doi.org/10.1038/leu.2012.367.*
55 55
2. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct 5;171(2):481-494.e15. doi: 10.1016/j.cell.2017.09.027. PMID: 28985567; PMCID: PMC5659841.*
56 56
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
57
+<!-- BL: paneaWholeGenomeLandscape2019 -->
58
+<!-- BL: paneaWholeGenomeLandscape2019 -->
59
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MECOM.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MECOM Expression
39 39
![image](images/gene_expression/MECOM_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MEF2B.md
... ...
@@ -6,9 +6,9 @@ MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
12 12
13 13
14 14
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -87,3 +87,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
87 87
88 88
89 89
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
90
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
91
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
92
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
93
+<!-- BL: 2 -->
MEF2C.md
... ...
@@ -6,8 +6,8 @@ MEF2C is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
10
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
50 50
## References
51 51
52 52
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
53
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
MET.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MET Expression
39 39
![image](images/gene_expression/MET_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MGA.md
... ...
@@ -6,7 +6,7 @@ MGA acts as a transcriptional repressor and interacts with MYC, a well-known onc
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -41,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
41 41
2. *Lee MJ, Koff JL, Switchenko JM, Jhaney CI, Harkins RA, Patel SP, Dave SS, Flowers CR. Genome-defined African ancestry is associated with distinct mutations and worse survival in patients with diffuse large B-cell lymphoma. Cancer. 2020 Aug 1;126(15):3493-3503. doi: 10.1002/cncr.32866. Epub 2020 May 29. PMID: 32469082; PMCID: PMC7494053.*
42 42
43 43
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
44
+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
45
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
MGEA5.md
... ...
@@ -6,7 +6,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|FL |2 |relevance in FL not firmly established|
9
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
MIR142.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -29,3 +29,5 @@
29 29
## MIR142 Expression
30 30
![image](images/gene_expression/MIR142_by_pathology.svg)
31 31
<!-- ORIGIN: kwanhianMicroRNA142Mutated202012b -->
32
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
33
+<!-- DLBCL: kwanhianMicroRNA142Mutated202012b -->
MIR155HG.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
MKI67.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|FL |2 |relevance in FL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -39,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
39 39
## MKI67 Expression
40 40
![image](images/gene_expression/MKI67_by_pathology.svg)
41 41
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
42
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
43
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
MME.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
## MME Expression
38 38
![image](images/gene_expression/MME_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
MPDZ.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MPDZ Expression
39 39
![image](images/gene_expression/MPDZ_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
42
+<!-- PMBL: reichelFlowSortingExome2015a -->
MPEG1.md
... ...
@@ -6,7 +6,7 @@ Mutations in MPEG1 have been described in DLBCL<sup>1</sup> with the overall rat
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
1. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
39 39
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
MRGPRF.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
35 35
## MRGPRF Expression
36 36
![image](images/gene_expression/MRGPRF_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
MS4A1.md
... ...
@@ -6,7 +6,7 @@ MS4A1 encodes the CD20 protein, which is the target of rituximab and other thera
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -40,4 +40,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
40 40
## MS4A1 Expression
41 41
![image](images/gene_expression/MS4A1_by_pathology.svg)
42 42
## References
43
-1. *Rushton CK, Arthur SE, Alcaide M, Cheung M, Jiang A, Coyle KM, Cleary KLS, Thomas N, Hilton LK, Michaud N, Daigle S, Davidson J, Bushell K, Yu S, Rys RN, Jain M, Shepherd L, Marra MA, Kuruvilla J, Crump M, Mann K, Assouline S, Connors JM, Steidl C, Cragg MS, Scott DW, Johnson NA, Morin RD. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv. 2020 Jul 14;4(13):2886-2898. doi: 10.1182/bloodadvances.2020001696. PMID: 32589730; PMCID: PMC7362366.*<!-- ORIGIN: rushtonGeneticEvolutionaryPatterns2020 -->
43
+<!-- ORIGIN: mottokIntegrativeGenomicAnalysis2019b -->
44
+<!-- DLBCL: rushtonGeneticEvolutionaryPatterns2020 -->
45
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
MSH2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MSH2 Expression
39 39
![image](images/gene_expression/MSH2_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MSH6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MSH6 Expression
39 39
![image](images/gene_expression/MSH6_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
MTOR.md
... ...
@@ -6,8 +6,8 @@ Although mutations in MTOR have been reported in DLBCL<sup>1</sup> and some BL,
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -54,3 +54,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
54 54
## References
55 55
56 56
1. *Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1398-403. doi: 10.1073/pnas.1205299110. Epub 2013 Jan 4. PMID: 23292937; PMCID: PMC3557051.*<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
57
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
58
+<!-- BL: paneaWholeGenomeLandscape2019 -->
MYB.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MYB Expression
39 39
![image](images/gene_expression/MYB_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
42
+<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
MYBPC2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MYBPC2 Expression
39 39
![image](images/gene_expression/MYBPC2_by_pathology.svg)
40 40
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
MYC.md
... ...
@@ -6,9 +6,9 @@ MYC is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |1-a | aSHM target and high-confidence BL gene |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
9
+|![BL](images/icons/BL_tier1.png) |1-a | aSHM target and high-confidence BL gene |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -86,4 +86,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
86 86
87 87
## References
88 88
89
-<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
89
+<!-- ORIGIN: johnstonCmycHypermutationBurkitt1992 -->
90
+<!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a -->
91
+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
92
+<!-- BL: johnstonCmycHypermutationBurkitt1992 -->
93
+<!-- BL: johnstonCmycHypermutationBurkitt1992 -->
MYCBP2.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------------------|
10
-|FL |2 |relevance in FL not firmly established|
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
MYH10.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
## MYH10 Expression
38 38
![image](images/gene_expression/MYH10_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
MYO18A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
## MYO18A Expression
38 38
![image](images/gene_expression/MYO18A_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
MYO1E.md
... ...
@@ -4,16 +4,12 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9 8
10 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:---------------------:|:-------------:|
14
-|BL |GAMBL genomes+capture|2.08 |
15
-|BL |Thomas cohort |1.30 |
16
-|BL |Panea cohort |4.00 |
17 13
|DLBCL |GAMBL genomes |2.49 |
18 14
|DLBCL |Schmitz cohort |3.40 |
19 15
|DLBCL |Reddy cohort |3.00 |
MYOM2.md
... ...
@@ -6,7 +6,7 @@ The prevalence of MYOM2 mutations in DLBCL varies across studies. The role of th
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
38 38
## MYOM2 Expression
39 39
![image](images/gene_expression/MYOM2_by_pathology.svg)
40 40
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
41
+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
N2RF2.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et a
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|-----------------------------------------|
10
-|DLBCL |2 |relevance in DLBCL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
NANOG.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NANOG Expression
39 39
![image](images/gene_expression/NANOG_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
NAV1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NAV1 Expression
39 39
![image](images/gene_expression/NAV1_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
NBEAL1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
## NBEAL1 Expression
38 38
![image](images/gene_expression/NBEAL1_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
NCOA3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -39,4 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
39 39
![image](images/proteinpaint/NCOA3.svg)
40 40
## NCOA3 Expression
41 41
![image](images/gene_expression/NCOA3_by_pathology.svg)
42
-<!-- ORIGIN: NA -->
42
+<!-- ORIGIN: Unknown -->
NCOR1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NCOR1 Expression
39 39
![image](images/gene_expression/NCOR1_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
NCOR2.md
... ...
@@ -6,8 +6,8 @@ Mutations in this gene are relatively rare in DLBCL overall but show a pattern o
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -52,3 +52,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
52 52
53 53
<!-- FLAGGED FOR TIER 2 -->
54 54
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
55
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
56
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
57
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
NEAT1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -36,3 +36,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
36 36
## NEAT1 Expression
37 37
![image](images/gene_expression/NEAT1_by_pathology.svg)
38 38
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
39
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
NF1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NF1 Expression
39 39
![image](images/gene_expression/NF1_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
NFKB1.md
... ...
@@ -6,7 +6,7 @@ Mutations in this gene are relatively rare in DLBCL overall. Some hotspots have
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -48,4 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
48 48
![image](images/gene_expression/NFKB1_by_pathology.svg)
49 49
50 50
<!-- FLAGGED FOR TIER 2 -->
51
-<!-- ORIGIN: NA -->
51
+<!-- ORIGIN: Unknown -->
NFKB2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NFKB2 Expression
39 39
![image](images/gene_expression/NFKB2_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
42
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
NFKBIA.md
... ...
@@ -6,17 +6,13 @@ NFKBIA encodes IκBα, an inhibitor of NF-κB, which regulates the NF-κB signal
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|FL |2 |relevance in FL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
15 14
|Entity|source |frequency (%)|
16 15
|:------:|:---------------------:|:-------------:|
17
-|BL |GAMBL genomes+capture|1.39 |
18
-|BL |Thomas cohort |1.70 |
19
-|BL |Panea cohort |2.00 |
20 16
|DLBCL |GAMBL genomes |4.40 |
21 17
|DLBCL |Schmitz cohort |3.83 |
22 18
|DLBCL |Reddy cohort |3.60 |
... ...
@@ -49,4 +45,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
49 45
50 46
## References
51 47
1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*
52
-<!-- ORIGIN: NA -->
48
+<!-- ORIGIN: lakeMutationsNFKBIAEncoding2009 -->
49
+<!-- DLBCL: lakeMutationsNFKBIAEncoding2009 -->
50
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
51
+<!-- PMBL: wienandGenomicAnalysesFlowsorted2019b -->
NFKBIE.md
... ...
@@ -6,8 +6,8 @@ NFKBIE encodes IκBε, a negative regulator of NF-κB. Mutations in NFKBIE can d
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
10
-|MCL |1 |high-confidence MCL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -46,3 +46,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
46 46
## References
47 47
1. *Mansouri, L., Noerenberg, D., Young, E., Mylonas, E., Abdulla, M., Frick, M., Asmar, F., Ljungström, V., Schneider, M., Yoshida, K., Skaftason, A., Pandzic, T., González, B., Tasidou, A., Waldhueter, N., Rivas-Delgado, A., Angelopoulou, M., Ziepert, M., Arends, C., Couronné, L., Lenze, D., Baldus, C., Bastard, C., Okosun, J., Fitzgibbon, J., Dörken, B., Drexler, H., Roos-Weil, D., Schmitt, C., Munch-Petersen, H., Zenz, T., Hansmann, M., Strefford, J., Enblad, G., Bernard, O., Ralfkiaer, E., Erlanson, M., Korkolopoulou, P., Hultdin, M., Papadaki, T., Grønbæk, K., López-Guillermo, A., Ogawa, S., Küppers, R., Stamatopoulos, K., Stavroyianni, N., Kanellis, G., Rosenwald, A., Campo, E., Amini, R., Ott, G., Vassilakopoulos, T., Hummel, M., Rosenquist, R., & Damm, F. (2016). Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma.. Blood, 128 23, 2666-2670 . https://doi.org/10.1182/BLOOD-2016-03-704528.*
48 48
2. *Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.*<!-- ORIGIN: morinGeneticLandscapesRelapsed2016 -->
49
+<!-- DLBCL: morinGeneticLandscapesRelapsed2016 -->
50
+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
51
+<!-- PMBL: mansouriFrequentNFKBIEDeletions2016 -->
NFKBIZ.md
... ...
@@ -6,7 +6,7 @@ The NFKBIZ gene is a significant player in NF-κB signaling, with mutations lead
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -49,3 +49,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
49 49
50 50
<!-- NONCODING -->
51 51
<!-- ORIGIN: morinGeneticLandscapesRelapsed2016 -->
52
+<!-- DLBCL: morinGeneticLandscapesRelapsed2016 -->
NIN.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
35 35
## NIN Expression
36 36
![image](images/gene_expression/NIN_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
NLRC5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,4 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
34 34
![image](images/proteinpaint/NLRC5.svg)
35 35
## NLRC5 Expression
36 36
![image](images/gene_expression/NLRC5_by_pathology.svg)
37
-<!-- ORIGIN: NA -->
37
+<!-- ORIGIN: Unknown -->
NLRP5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NLRP5 Expression
39 39
![image](images/gene_expression/NLRP5_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
NLRP8.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 38
## NLRP8 Expression
39 39
![image](images/gene_expression/NLRP8_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
NOA1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
## NOA1 Expression
38 38
![image](images/gene_expression/NOA1_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
NOL9.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -42,4 +42,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
42 42
![image](images/proteinpaint/NOL9.svg)
43 43
## NOL9 Expression
44 44
![image](images/gene_expression/NOL9_by_pathology.svg)
45
-<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
45
+<!-- ORIGIN: spinaGeneticsNodalMarginal2016b -->
46
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
47
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
NOTCH1.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|MCL |1 |high-confidence MCL gene |
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -50,3 +50,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
50 50
## NOTCH1 Expression
51 51
![image](images/gene_expression/NOTCH1_by_pathology.svg)
52 52
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
53
+<!-- BL: loveGeneticLandscapeMutations2012 -->
54
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
55
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
56
+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
NOTCH2.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|MCL |1 |high-confidence MCL gene |
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -48,4 +48,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
48 48
![image](images/proteinpaint/NOTCH2.svg)
49 49
## NOTCH2 Expression
50 50
![image](images/gene_expression/NOTCH2_by_pathology.svg)
51
-<!-- ORIGIN: troenNOTCH2MutationsMarginal2008 -->
51
+<!-- ORIGIN: 18508802 -->
52
+<!-- DLBCL: troenNOTCH2MutationsMarginal2008 -->
53
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
54
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
55
+<!-- BL: paneaWholeGenomeLandscape2019 -->
NRXN2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
## NRXN2 Expression
38 38
![image](images/gene_expression/NRXN2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
NSD2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
31 31
## NSD2 Expression
32 32
![image](images/gene_expression/NSD2_by_pathology.svg)
33 33
<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
34
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
ODZ3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -25,3 +25,4 @@
25 25
## ODZ3 Expression
26 26
![image](images/gene_expression/ODZ3_by_pathology.svg)
27 27
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
28
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
OGDHL.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
35 35
## OGDHL Expression
36 36
![image](images/gene_expression/OGDHL_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
OR8H2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
35 35
## OR8H2 Expression
36 36
![image](images/gene_expression/OR8H2_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
OSBPL10.md
... ...
@@ -6,16 +6,12 @@ OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11 10
12 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 12
14 13
|Entity|source |frequency (%)|
15 14
|:------:|:---------------------:|:-------------:|
16
-|BL |GAMBL genomes+capture| 2.08 |
17
-|BL |Thomas cohort | 2.10 |
18
-|BL |Panea cohort | 3.00 |
19 15
|DLBCL |GAMBL genomes | 8.80 |
20 16
|DLBCL |Schmitz cohort |14.26 |
21 17
|DLBCL |Reddy cohort | 2.30 |
... ...
@@ -46,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
46 42
## OSBPL10 Expression
47 43
![image](images/gene_expression/OSBPL10_by_pathology.svg)
48 44
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
45
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
P2RX5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
43 43
## P2RX5 Expression
44 44
![image](images/gene_expression/P2RX5_by_pathology.svg)
45 45
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
46
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
P2RY2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## P2RY2 Expression
38 38
![image](images/gene_expression/P2RY2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
P2RY8.md
... ...
@@ -5,9 +5,9 @@ P2RY8 encodes a G protein–coupled receptor that is expressed on germinal cente
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------------------|
8
-|BL |1 |high-confidence BL gene |
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |2 |relevance in FL not firmly established|
8
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -47,3 +47,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 47
2. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.*
48 48
49 49
<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->
50
+<!-- BL: muppidiLossSignalingGa132014b -->
51
+<!-- DLBCL: lohrDiscoveryPrioritizationSomatic2012a -->
PABPC4L.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PABPC4L Expression
38 38
![image](images/gene_expression/PABPC4L_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
PAPOLG.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PAPOLG Expression
39 39
![image](images/gene_expression/PAPOLG_by_pathology.svg)
40 40
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
PASK.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PASK Expression
39 39
![image](images/gene_expression/PASK_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
PAX5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -47,3 +47,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 47
## PAX5 Expression
48 48
![image](images/gene_expression/PAX5_by_pathology.svg)
49 49
<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
50
+<!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a -->
PC.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PC Expression
38 38
![image](images/gene_expression/PC_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
PCBP1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![BL](images/icons/BL_tier2.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -50,4 +50,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
50 50
![image](images/proteinpaint/PCBP1.svg)
51 51
## PCBP1 Expression
52 52
![image](images/gene_expression/PCBP1_by_pathology.svg)
53
-<!-- ORIGIN: NA -->
53
+<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
54
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
PCDHA11.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PCDHA11 Expression
38 38
![image](images/gene_expression/PCDHA11_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
PCDHB11.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PCDHB11 Expression
39 39
![image](images/gene_expression/PCDHB11_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
PCDHB2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
35 35
## PCDHB2 Expression
36 36
![image](images/gene_expression/PCDHB2_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
PCLO.md
... ...
@@ -5,8 +5,8 @@
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|-----------------------------------------|
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
-|FL |1 |high-confidence FL gene |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -51,3 +51,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
51 51
52 52
53 53
<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->
54
+<!-- DLBCL: lohrDiscoveryPrioritizationSomatic2012a -->
PDCD11.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PDCD11 Expression
38 38
![image](images/gene_expression/PDCD11_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
PDE4DIP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PDE4DIP Expression
39 39
![image](images/gene_expression/PDE4DIP_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
PDS5B.md
... ...
@@ -6,8 +6,8 @@ Mutations in this gene were first described in DLBCL in 2013 by Morin et al<sup>
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|-----------------------------------------|
9
-|DLBCL |2 |relevance in DLBCL not firmly established|
10
-|FL |2 |relevance in FL not firmly established |
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
PDZRN3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PDZRN3 Expression
38 38
![image](images/gene_expression/PDZRN3_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
PHF6.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -42,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
42 42
## PHF6 Expression
43 43
![image](images/gene_expression/PHF6_by_pathology.svg)
44 44
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
45
+<!-- BL: thomasGeneticSubgroupsInform2023 -->
46
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
PIK3CD.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
44 44
## PIK3CD Expression
45 45
![image](images/gene_expression/PIK3CD_by_pathology.svg)
46 46
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
47
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
PIK3R1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -42,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
42 42
## PIK3R1 Expression
43 43
![image](images/gene_expression/PIK3R1_by_pathology.svg)
44 44
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
45
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
46
+<!-- BL: paneaWholeGenomeLandscape2019 -->
PIM1.md
... ...
@@ -6,9 +6,9 @@ PIM1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -76,3 +76,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
76 76
## PIM1 Expression
77 77
![image](images/gene_expression/PIM1_by_pathology.svg)
78 78
<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
79
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
80
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
81
+<!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a -->
PIM2.md
... ...
@@ -6,7 +6,7 @@ PIM2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -41,4 +41,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
41 41
![image](images/proteinpaint/PIM2.svg)
42 42
## PIM2 Expression
43 43
![image](images/gene_expression/PIM2_by_pathology.svg)
44
-<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
44
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
45
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
46
+<!-- PMBL: reichelFlowSortingExome2015a -->
PKD1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PKD1 Expression
39 39
![image](images/gene_expression/PKD1_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
PLCG2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
43 43
## PLCG2 Expression
44 44
![image](images/gene_expression/PLCG2_by_pathology.svg)
45 45
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
46
+<!-- BL: paneaWholeGenomeLandscape2019 -->
PLXNB3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
35 35
## PLXNB3 Expression
36 36
![image](images/gene_expression/PLXNB3_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
39
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
PMAIP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,3 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
34 34
## PMAIP1 Expression
35 35
![image](images/gene_expression/PMAIP1_by_pathology.svg)
36 36
<!-- ORIGIN: Unknown -->
37
+<!-- BL: 2 -->
PNPO.md
... ...
@@ -6,7 +6,7 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|-----------------------------------------|
9
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
POGZ.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## POGZ Expression
39 39
![image](images/gene_expression/POGZ_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
POLRMT.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## POLRMT Expression
38 38
![image](images/gene_expression/POLRMT_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
POR.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## POR Expression
38 38
![image](images/gene_expression/POR_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
POT1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
35 35
## POT1 Expression
36 36
![image](images/gene_expression/POT1_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
POU2AF1.md
... ...
@@ -6,8 +6,8 @@ POU2AF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
10
-|FL |1-a |high-confidence FL gene, hypermutated |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated|
10
+|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated |
11 11
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -54,4 +54,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
54 54
![image](images/proteinpaint/POU2AF1.svg)
55 55
## POU2AF1 Expression
56 56
![image](images/gene_expression/POU2AF1_by_pathology.svg)
57
-<!-- ORIGIN: NA -->
57
+<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
58
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
POU2F2.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
8
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -47,3 +47,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 47
## POU2F2 Expression
48 48
![image](images/gene_expression/POU2F2_by_pathology.svg)
49 49
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
50
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
51
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
PPP1R9B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL | 2 | low-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) | 2 | low-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -36,4 +36,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
36 36
37 37
<!-- FLAGGED FOR TIER 2 -->
38 38
39
-<!-- ORIGIN: NA -->
39
+<!-- ORIGIN: Unknown -->
PPP4C.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
40 40
## PPP4C Expression
41 41
![image](images/gene_expression/PPP4C_by_pathology.svg)
42 42
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
43
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
PPP6R2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PPP6R2 Expression
38 38
![image](images/gene_expression/PPP6R2_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
PRDM1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
PREX1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PREX1 Expression
38 38
![image](images/gene_expression/PREX1_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
PRKCB.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PRKCB Expression
39 39
![image](images/gene_expression/PRKCB_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
PRKDC.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene |
8
-|FL |2 |relevance in FL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -40,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
40 40
## PRKDC Expression
41 41
![image](images/gene_expression/PRKDC_by_pathology.svg)
42 42
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
43
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
44
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
PRPS1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PRPS1 Expression
39 39
![image](images/gene_expression/PRPS1_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
PRSS22.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PRSS22 Expression
38 38
![image](images/gene_expression/PRSS22_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
PTEN.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
PTMA.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
PTPN1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -39,4 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 39
![image](images/proteinpaint/PTPN1.svg)
40 40
## PTPN1 Expression
41 41
![image](images/gene_expression/PTPN1_by_pathology.svg)
42
-<!-- ORIGIN: NA -->
42
+<!-- ORIGIN: gunawardanaRecurrentSomaticMutations2014c -->
43
+<!-- PMBL: gunawardanaRecurrentSomaticMutations2014c -->
PTPN23.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PTPN23 Expression
39 39
![image](images/gene_expression/PTPN23_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
PTPN6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PTPN6 Expression
39 39
![image](images/gene_expression/PTPN6_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
PTPRD.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
8
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -43,4 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
43 43
![image](images/proteinpaint/PTPRD.svg)
44 44
## PTPRD Expression
45 45
![image](images/gene_expression/PTPRD_by_pathology.svg)
46
-<!-- ORIGIN: NA -->
46
+<!-- ORIGIN: spinaGeneticsNodalMarginal2016b -->
47
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
PTPRK.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
## PTPRK Expression
39 39
![image](images/gene_expression/PTPRK_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
PTPRN.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PTPRN Expression
38 38
![image](images/gene_expression/PTPRN_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
PXDNL.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
## PXDNL Expression
38 38
![image](images/gene_expression/PXDNL_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
PZP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
35 35
## PZP Expression
36 36
![image](images/gene_expression/PZP_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
RAC2.md
... ...
@@ -1,11 +1,13 @@
1 1
# RAC2
2
+## History
3
+Mutations in this gene were first described in BL in 2019 by Panea et al<sup>1</sup> and in DLBCL 2021 by Hübschmann et al.<sup>2</sup>
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 11
10 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 13
... ...
@@ -27,11 +29,6 @@
27 29
|DLBCL |No |No |6.256 |0 |
28 30
|FL |No |No |0.000 |0 |
29 31
30
-
31
-> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
33
-
34
-
35 32
## RAC2 Hotspots
36 33
37 34
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -49,4 +46,13 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
49 46
![image](images/proteinpaint/RAC2.svg)
50 47
## RAC2 Expression
51 48
![image](images/gene_expression/RAC2_by_pathology.svg)
52
-<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
49
+
50
+## References
51
+
52
+1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
53
+
54
+2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
55
+
56
+<!-- ORIGIN: 33953289 -->
57
+<!-- BL: paneaWholeGenomeLandscape2019 -->
58
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
RAD9A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 38
## RAD9A Expression
39 39
![image](images/gene_expression/RAD9A_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
RANBP6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
## RANBP6 Expression
38 38
![image](images/gene_expression/RANBP6_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
RARA.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 38
## RARA Expression
39 39
![image](images/gene_expression/RARA_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
RB1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
8
-|MCL |1 |high-confidence MCL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -40,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
40 40
## RB1 Expression
41 41
![image](images/gene_expression/RB1_by_pathology.svg)
42 42
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
43
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
44
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
RBM6.md
... ...
@@ -1,10 +1,12 @@
1 1
# RBM6
2
+## History
3
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
9
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 10
9 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
... ...
@@ -21,10 +23,6 @@
21 23
|FL |No |No |0.00 |0 |
22 24
23 25
24
-> [!NOTE]
25
-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
26
-
27
-
28 26
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RBM6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RBM6_protein_hg38.html)
29 27
30 28
![image](images/proteinpaint/RBM6_NM_005777.svg)
... ...
@@ -34,4 +32,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
34 32
![image](images/proteinpaint/RBM6.svg)
35 33
## RBM6 Expression
36 34
![image](images/gene_expression/RBM6_by_pathology.svg)
35
+
36
+## References
37
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
38
+
37 39
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
40
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
RBP3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
## RBP3 Expression
38 38
![image](images/gene_expression/RBP3_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
RET.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
## RET Expression
38 38
![image](images/gene_expression/RET_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
REV3L.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
## REV3L Expression
38 38
![image](images/gene_expression/REV3L_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
RFTN1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
43 43
## RFTN1 Expression
44 44
![image](images/gene_expression/RFTN1_by_pathology.svg)
45 45
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46
+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
47
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
RFX7.md
... ...
@@ -1,11 +1,13 @@
1 1
# RFX7
2
+## History
3
+First described as mutated in BL in 2009 by Grande et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9 11
10 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 13
... ...
@@ -36,6 +38,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
36 38
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFX7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFX7_hg38.html)
37 39
38 40
![image](images/proteinpaint/RFX7.svg)
41
+
39 42
## RFX7 Expression
40 43
![image](images/gene_expression/RFX7_by_pathology.svg)
41
-<!-- ORIGIN: NA -->
44
+
45
+## References
46
+1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
47
+
48
+<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
49
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
RFXAP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
RHEX.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
RHOA.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -53,3 +53,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
53 53
## RHOA Expression
54 54
![image](images/gene_expression/RHOA_by_pathology.svg)
55 55
<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
56
+<!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a -->
57
+<!-- BL: richterRecurrentMutationID32012a -->
RHOH.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
RNF144B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
7
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
42 42
## RNF144B Expression
43 43
![image](images/gene_expression/RNF144B_by_pathology.svg)
44 44
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
45
+<!-- BL: paneaWholeGenomeLandscape2019 -->
ROBO2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -26,3 +26,4 @@
26 26
## ROBO2 Expression
27 27
![image](images/gene_expression/ROBO2_by_pathology.svg)
28 28
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
29
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
RPL10.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
## RPL10 Expression
38 38
![image](images/gene_expression/RPL10_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
RPL22.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,3 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
34 34
## RPL22 Expression
35 35
![image](images/gene_expression/RPL22_by_pathology.svg)
36 36
<!-- ORIGIN: Unknown -->
37
+<!-- BL: 2 -->
RRAGC.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
8
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
40 40
## RRAGC Expression
41 41
![image](images/gene_expression/RRAGC_by_pathology.svg)
42 42
<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
43
+<!-- DLBCL: okosunRecurrentMTORC1activatingRRAGC2016a -->
RUBCNL.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
RUNX1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 38
## RUNX1 Expression
39 39
![image](images/gene_expression/RUNX1_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
S1PR1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## S1PR1 Expression
36 36
![image](images/gene_expression/S1PR1_by_pathology.svg)
37 37
<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
38
+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
S1PR2.md
... ...
@@ -6,9 +6,9 @@ S1PR2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -50,4 +50,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
50 50
![image](images/proteinpaint/S1PR2.svg)
51 51
## S1PR2 Expression
52 52
![image](images/gene_expression/S1PR2_by_pathology.svg)
53
-<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
53
+<!-- ORIGIN: 21796119 -->
54
+<!-- BL: muppidiLossSignalingGa132014b -->
55
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
SAL3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
31 31
## SAL3 Expression
32 32
![image](images/gene_expression/SAL3_by_pathology.svg)
33 33
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
34
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
SALL3.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|MCL |2 |relevance in MCL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
8
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -39,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
39 39
## SALL3 Expression
40 40
![image](images/gene_expression/SALL3_by_pathology.svg)
41 41
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
42
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
43
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SAMD9L.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## SAMD9L Expression
39 39
![image](images/gene_expression/SAMD9L_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
SAPS2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
31 31
## SAPS2 Expression
32 32
![image](images/gene_expression/SAPS2_by_pathology.svg)
33 33
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SARM1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## SARM1 Expression
39 39
![image](images/gene_expression/SARM1_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
SBF1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SBF1 Expression
38 38
![image](images/gene_expression/SBF1_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SEL1L3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
SEPT10.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,3 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
34 34
## SEPT10 Expression
35 35
![image](images/gene_expression/SEPT10_by_pathology.svg)
36 36
<!-- ORIGIN: Unknown -->
37
+<!-- BL: 2 -->
SEPTIN9.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
SERPINA9.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
43 43
## SERPINA9 Expression
44 44
![image](images/gene_expression/SERPINA9_by_pathology.svg)
45 45
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
SESN1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
SETD1B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
45 45
## SETD1B Expression
46 46
![image](images/gene_expression/SETD1B_by_pathology.svg)
47 47
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
48
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
SETD2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SETD2 Expression
36 36
![image](images/gene_expression/SETD2_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
38
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
SETD5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -41,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
41 41
## SETD5 Expression
42 42
![image](images/gene_expression/SETD5_by_pathology.svg)
43 43
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
44
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
45
+<!-- PMBL: tiacciPervasiveMutationsJAKSTAT2018b -->
SF3B1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
50 50
## SF3B1 Expression
51 51
![image](images/gene_expression/SF3B1_by_pathology.svg)
52 52
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
53
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SGK1.md
... ...
@@ -4,17 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
-|FL |1-a | aSHM target and high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
10 9
11 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 11
13 12
|Entity|source |frequency (%)|
14 13
|:------:|:---------------------:|:-------------:|
15
-|BL |GAMBL genomes+capture| 2.08 |
16
-|BL |Thomas cohort | 2.50 |
17
-|BL |Panea cohort | 4.00 |
18 14
|DLBCL |GAMBL genomes |11.09 |
19 15
|DLBCL |Schmitz cohort |10.64 |
20 16
|DLBCL |Reddy cohort |11.21 |
... ...
@@ -53,3 +49,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
53 49
## SGK1 Expression
54 50
![image](images/gene_expression/SGK1_by_pathology.svg)
55 51
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
52
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
53
+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
54
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
SHANK1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SHANK1 Expression
38 38
![image](images/gene_expression/SHANK1_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SHROOM3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SHROOM3 Expression
36 36
![image](images/gene_expression/SHROOM3_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
SI.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SI Expression
36 36
![image](images/gene_expression/SI_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
SIAH2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
SLC29A2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SLC29A2 Expression
38 38
![image](images/gene_expression/SLC29A2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SLC34A2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## SLC34A2 Expression
39 39
![image](images/gene_expression/SLC34A2_by_pathology.svg)
40 40
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
41
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
SMARCA4.md
... ...
@@ -4,10 +4,10 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
9
-|FL |1 |high-confidence FL gene |
10
-|MCL |1 |high-confidence MCL gene |
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
... ...
@@ -45,4 +45,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
45 45
![image](images/proteinpaint/SMARCA4.svg)
46 46
## SMARCA4 Expression
47 47
![image](images/gene_expression/SMARCA4_by_pathology.svg)
48
-<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
48
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
49
+<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
50
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
51
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
52
+<!-- BL: richterRecurrentMutationID32012a -->
SMARCB1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SMARCB1 Expression
36 36
![image](images/gene_expression/SMARCB1_by_pathology.svg)
37 37
<!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a -->
38
+<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
SMC1A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SMC1A Expression
36 36
![image](images/gene_expression/SMC1A_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
SMEK1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## SMEK1 Expression
39 39
![image](images/gene_expression/SMEK1_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
SNTB2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SNTB2 Expression
38 38
![image](images/gene_expression/SNTB2_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
SOCS1.md
... ...
@@ -4,17 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
-|FL |1-a | aSHM target and high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
10 9
11 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 11
13 12
|Entity|source |frequency (%)|
14 13
|:------:|:---------------------:|:-------------:|
15
-|BL |GAMBL genomes+capture| 1.85 |
16
-|BL |Thomas cohort | 1.70 |
17
-|BL |Panea cohort | 3.00 |
18 14
|DLBCL |GAMBL genomes |15.30 |
19 15
|DLBCL |Schmitz cohort |12.77 |
20 16
|DLBCL |Reddy cohort |10.41 |
... ...
@@ -45,4 +41,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
45 41
![image](images/proteinpaint/SOCS1.svg)
46 42
## SOCS1 Expression
47 43
![image](images/gene_expression/SOCS1_by_pathology.svg)
48
-<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
44
+<!-- ORIGIN: wenigerMutationsTumorSuppressor2006a -->
45
+<!-- PMBL: wenigerMutationsTumorSuppressor2006a -->
46
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
SP140.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SP140 Expression
36 36
![image](images/gene_expression/SP140_by_pathology.svg)
37 37
<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
38
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
SP3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SP3 Expression
38 38
![image](images/gene_expression/SP3_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
SPEN.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
43 43
## SPEN Expression
44 44
![image](images/gene_expression/SPEN_by_pathology.svg)
45 45
<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
46
+<!-- DLBCL: rossiCodingGenomeSplenic2012c -->
47
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
48
+<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
SRRM2.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
8
-|FL |2 |relevance in FL not firmly established |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -40,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
40 40
## SRRM2 Expression
41 41
![image](images/gene_expression/SRRM2_by_pathology.svg)
42 42
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
43
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
44
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
ST6GAL1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
43 43
## ST6GAL1 Expression
44 44
![image](images/gene_expression/ST6GAL1_by_pathology.svg)
45 45
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
STAB2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## STAB2 Expression
36 36
![image](images/gene_expression/STAB2_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
STAT3.md
... ...
@@ -4,16 +4,12 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9 8
10 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:---------------------:|:-------------:|
14
-|BL |GAMBL genomes+capture|0.92 |
15
-|BL |Thomas cohort |0.00 |
16
-|BL |Panea cohort |1.00 |
17 13
|DLBCL |GAMBL genomes |7.07 |
18 14
|DLBCL |Schmitz cohort |9.36 |
19 15
|DLBCL |Reddy cohort |3.60 |
... ...
@@ -50,3 +46,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
50 46
## STAT3 Expression
51 47
![image](images/gene_expression/STAT3_by_pathology.svg)
52 48
<!-- ORIGIN: ohgamiSTAT3MutationsAre2014 -->
49
+<!-- DLBCL: ohgamiSTAT3MutationsAre2014 -->
STAT5B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## STAT5B Expression
39 39
![image](images/gene_expression/STAT5B_by_pathology.svg)
40 40
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41
+<!-- PMBL: tiacciPervasiveMutationsJAKSTAT2018b -->
42
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
STAT6.md
... ...
@@ -6,17 +6,13 @@ The STAT6 gene, which encodes a transcription factor involved in the JAK-STAT si
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|FL |1 |high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
15 14
|Entity|source |frequency (%)|
16 15
|:------:|:---------------------:|:-------------:|
17
-|BL |GAMBL genomes+capture| 1.62 |
18
-|BL |Thomas cohort | 1.70 |
19
-|BL |Panea cohort | 2.00 |
20 16
|DLBCL |GAMBL genomes | 5.74 |
21 17
|DLBCL |Schmitz cohort | 2.55 |
22 18
|DLBCL |Reddy cohort | 3.80 |
... ...
@@ -67,3 +63,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
67 63
## STAT6 Expression
68 64
![image](images/gene_expression/STAT6_by_pathology.svg)
69 65
<!-- ORIGIN: yildizActivatingSTAT6Mutations2015c -->
66
+<!-- PMBL: ritzRecurrentMutationsSTAT62009a -->
67
+<!-- FL: yildizActivatingSTAT6Mutations2015c -->
68
+<!-- DLBCL: yildizActivatingSTAT6Mutations2015c -->
SYK.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## SYK Expression
39 39
![image](images/gene_expression/SYK_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
SYNCRIP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SYNCRIP Expression
38 38
![image](images/gene_expression/SYNCRIP_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
SYNE1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SYNE1 Expression
36 36
![image](images/gene_expression/SYNE1_by_pathology.svg)
37 37
<!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a -->
38
+<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
SYNGAP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
## SYNGAP1 Expression
38 38
![image](images/gene_expression/SYNGAP1_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
SYPL1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 38
## SYPL1 Expression
39 39
![image](images/gene_expression/SYPL1_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
TAF1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
38 38
## TAF1 Expression
39 39
![image](images/gene_expression/TAF1_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
42
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
TAP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
38 38
## TAP1 Expression
39 39
![image](images/gene_expression/TAP1_by_pathology.svg)
40 40
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
TBC1D26.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
35 35
## TBC1D26 Expression
36 36
![image](images/gene_expression/TBC1D26_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
TBC1D4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
40 40
## TBC1D4 Expression
41 41
![image](images/gene_expression/TBC1D4_by_pathology.svg)
42 42
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
43
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
TBC1D9B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
## TBC1D9B Expression
38 38
![image](images/gene_expression/TBC1D9B_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
TBL1XR1.md
... ...
@@ -4,17 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10 9
11 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 11
13 12
|Entity|source |frequency (%)|
14 13
|:------:|:---------------------:|:-------------:|
15
-|BL |GAMBL genomes+capture| 6.00 |
16
-|BL |Thomas cohort | 4.70 |
17
-|BL |Panea cohort | 7.90 |
18 14
|DLBCL |GAMBL genomes | 8.60 |
19 15
|DLBCL |Schmitz cohort |12.77 |
20 16
|DLBCL |Reddy cohort | 5.71 |
... ...
@@ -56,4 +52,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
56 52
![image](images/proteinpaint/TBL1XR1.svg)
57 53
## TBL1XR1 Expression
58 54
![image](images/gene_expression/TBL1XR1_by_pathology.svg)
59
-<!-- ORIGIN: mareschalWholeExomeSequencing2016 -->
55
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
56
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
57
+<!-- DLBCL: mareschalWholeExomeSequencing2016 -->
TCF3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|BL |1 |high-confidence BL gene|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
50 50
## TCF3 Expression
51 51
![image](images/gene_expression/TCF3_by_pathology.svg)
52 52
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
53
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
TCL1A.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |1-a | aSHM target and high-confidence BL gene |
8
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
7
+|![BL](images/icons/BL_tier1.png) |1-a | aSHM target and high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |1-a | aSHM target and high-confidence DLBCL gene|
9 9
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -51,4 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
51 51
52 52
## References
53 53
1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.*
54
-<!-- ORIGIN: NA -->
54
+<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
55
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
TERT.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
35 35
## TERT Expression
36 36
![image](images/gene_expression/TERT_by_pathology.svg)
37 37
<!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a -->
38
+<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
TET2.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -41,4 +41,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
41 41
![image](images/proteinpaint/TET2.svg)
42 42
## TET2 Expression
43 43
![image](images/gene_expression/TET2_by_pathology.svg)
44
-<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
44
+<!-- ORIGIN: 28327945 -->
45
+<!-- BL: paneaWholeGenomeLandscape2019 -->
46
+<!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a -->
TGFBR2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
38 38
## TGFBR2 Expression
39 39
![image](images/gene_expression/TGFBR2_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
TIGD6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
## TIGD6 Expression
38 38
![image](images/gene_expression/TIGD6_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
TIPARP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
38 38
## TIPARP Expression
39 39
![image](images/gene_expression/TIPARP_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
TLR2.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
8
-|MCL |1 |high-confidence MCL gene |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -47,3 +47,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
47 47
## TLR2 Expression
48 48
![image](images/gene_expression/TLR2_by_pathology.svg)
49 49
<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
50
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
51
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
TMEM30A.md
... ...
@@ -4,17 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |2 |relevance in FL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
10 9
11 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 11
13 12
|Entity|source |frequency (%)|
14 13
|:------:|:---------------------:|:-------------:|
15
-|BL |GAMBL genomes+capture|1.85 |
16
-|BL |Thomas cohort |1.30 |
17
-|BL |Panea cohort |5.00 |
18 14
|DLBCL |GAMBL genomes |4.78 |
19 15
|DLBCL |Schmitz cohort |7.66 |
20 16
|DLBCL |Reddy cohort |2.80 |
... ...
@@ -54,3 +50,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
54 50
## TMEM30A Expression
55 51
![image](images/gene_expression/TMEM30A_by_pathology.svg)
56 52
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
53
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
54
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
TMSB4X.md
... ...
@@ -6,17 +6,13 @@ TMSB4X is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
-|FL |1-a | aSHM target and high-confidence FL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
15 14
|Entity|source |frequency (%)|
16 15
|:------:|:---------------------:|:-------------:|
17
-|BL |GAMBL genomes+capture| 0.69 |
18
-|BL |Thomas cohort | 0.00 |
19
-|BL |Panea cohort | 2.00 |
20 16
|DLBCL |GAMBL genomes |12.43 |
21 17
|DLBCL |Schmitz cohort |20.85 |
22 18
|DLBCL |Reddy cohort |13.11 |
... ...
@@ -51,3 +47,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
51 47
## TMSB4X Expression
52 48
![image](images/gene_expression/TMSB4X_by_pathology.svg)
53 49
<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
50
+<!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a -->
TNFAIP3.md
... ...
@@ -4,17 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10 9
11 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 11
13 12
|Entity|source |frequency (%)|
14 13
|:------:|:---------------------:|:-------------:|
15
-|BL |GAMBL genomes+capture| 1.39 |
16
-|BL |Thomas cohort | 0.80 |
17
-|BL |Panea cohort | 2.00 |
18 14
|DLBCL |GAMBL genomes | 6.69 |
19 15
|DLBCL |Schmitz cohort |16.60 |
20 16
|DLBCL |Reddy cohort | 8.11 |
... ...
@@ -56,4 +52,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
56 52
## References
57 53
1.
58 54
2. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
59
-<!-- ORIGIN: compagnoMutationsMultipleGenes2009a -->
55
+<!-- ORIGIN: rossiAlterationBIRC3Multiple2011a -->
56
+<!-- PMBL: schmitzTNFAIP3A20Tumor2009a -->
57
+<!-- DLBCL: compagnoMutationsMultipleGenes2009a -->
58
+<!-- MZL: rossiAlterationBIRC3Multiple2011a -->
TNFRSF14.md
... ...
@@ -4,17 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |1 |high-confidence FL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
10 9
11 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 11
13 12
|Entity|source |frequency (%)|
14 13
|:------:|:---------------------:|:-------------:|
15
-|BL |GAMBL genomes+capture| 1.39 |
16
-|BL |Thomas cohort | 0.80 |
17
-|BL |Panea cohort | 3.00 |
18 14
|DLBCL |GAMBL genomes |14.34 |
19 15
|DLBCL |Schmitz cohort |16.81 |
20 16
|DLBCL |Reddy cohort | 9.71 |
... ...
@@ -65,3 +61,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
65 61
1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Ch$
66 62
67 63
<!-- ORIGIN: cheungAcquiredTNFRSF14Mutations2010a -->
64
+<!-- FL: cheungAcquiredTNFRSF14Mutations2010a -->
65
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
66
+<!-- DLBCL: cheungAcquiredTNFRSF14Mutations2010a -->
TOP2A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
## TOP2A Expression
38 38
![image](images/gene_expression/TOP2A_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
TOX.md
... ...
@@ -4,16 +4,12 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9 8
10 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:---------------------:|:-------------:|
14
-|BL |GAMBL genomes+capture|2.08 |
15
-|BL |Thomas cohort |0.80 |
16
-|BL |Panea cohort |5.90 |
17 13
|DLBCL |GAMBL genomes |4.21 |
18 14
|DLBCL |Schmitz cohort |5.53 |
19 15
|DLBCL |Reddy cohort |4.00 |
... ...
@@ -48,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
48 44
## TOX Expression
49 45
![image](images/gene_expression/TOX_by_pathology.svg)
50 46
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
47
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
TP53.md
... ...
@@ -5,10 +5,10 @@
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------|
8
-|BL |1 |high-confidence BL gene |
9
-|DLBCL |1 |high-confidence DLBCL gene|
10
-|FL |1 |high-confidence FL gene |
11
-|MCL |1 |high-confidence MCL gene |
8
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
11
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -50,4 +50,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
50 50
51 51
## References
52 52
1.
53
-<!-- ORIGIN: NA -->
53
+<!-- ORIGIN: wildaInactivationARFMDM2p53Pathway2004 -->
54
+<!-- BL: wildaInactivationARFMDM2p53Pathway2004 -->
55
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
56
+<!-- BL: wildaInactivationARFMDM2p53Pathway2004 -->
57
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
58
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
TPP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
35 35
## TPP1 Expression
36 36
![image](images/gene_expression/TPP1_by_pathology.svg)
37 37
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
38
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
TPST2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
## TPST2 Expression
38 38
![image](images/gene_expression/TPST2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
TRAF3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,4 +37,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
![image](images/proteinpaint/TRAF3.svg)
38 38
## TRAF3 Expression
39 39
![image](images/gene_expression/TRAF3_by_pathology.svg)
40
-<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
40
+<!-- ORIGIN: rossiAlterationBIRC3Multiple2011a -->
41
+<!-- MZL: rossiAlterationBIRC3Multiple2011a -->
42
+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
43
+<!-- PMBL: ottoGeneticLesionsTRAF32012a -->
TRAF6.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -46,3 +46,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
46 46
## TRAF6 Expression
47 47
![image](images/gene_expression/TRAF6_by_pathology.svg)
48 48
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
49
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
TRIP12.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,4 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
34 34
![image](images/proteinpaint/TRIP12.svg)
35 35
## TRIP12 Expression
36 36
![image](images/gene_expression/TRIP12_by_pathology.svg)
37
-<!-- ORIGIN: NA -->
37
+<!-- ORIGIN: Unknown -->
TRRAP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -41,4 +41,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
41 41
![image](images/proteinpaint/TRRAP.svg)
42 42
## TRRAP Expression
43 43
![image](images/gene_expression/TRRAP_by_pathology.svg)
44
-<!-- ORIGIN: NA -->
44
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
45
+<!-- DLBCL: parryWholeExomeSequencing2013 -->
46
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
TTN.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
43 43
## TTN Expression
44 44
![image](images/gene_expression/TTN_by_pathology.svg)
45 45
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
46
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
UBE2A.md
... ...
@@ -4,16 +4,12 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
9 8
10 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:---------------------:|:-------------:|
14
-|BL |GAMBL genomes+capture|0.92 |
15
-|BL |Thomas cohort |0.00 |
16
-|BL |Panea cohort |3.00 |
17 13
|DLBCL |GAMBL genomes |4.21 |
18 14
|DLBCL |Schmitz cohort |7.02 |
19 15
|DLBCL |Reddy cohort |3.90 |
... ...
@@ -38,4 +34,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
38 34
![image](images/proteinpaint/UBE2A.svg)
39 35
## UBE2A Expression
40 36
![image](images/gene_expression/UBE2A_by_pathology.svg)
41
-<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
37
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
38
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
39
+<!-- PMBL: reichelFlowSortingExome2015a -->
UBE2J1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
UBR5.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
8
-|MCL |1 |high-confidence MCL gene |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -40,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
40 40
## UBR5 Expression
41 41
![image](images/gene_expression/UBR5_by_pathology.svg)
42 42
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
43
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
44
+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
UNC5B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
38 38
## UNC5B Expression
39 39
![image](images/gene_expression/UNC5B_by_pathology.svg)
40 40
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
41
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
UNC5C.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -34,4 +34,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
34 34
![image](images/proteinpaint/UNC5C.svg)
35 35
## UNC5C Expression
36 36
![image](images/gene_expression/UNC5C_by_pathology.svg)
37
-<!-- ORIGIN: NA -->
37
+<!-- ORIGIN: Unknown -->
UNC5D.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL | 2 |low-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) | 2 |low-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -36,4 +36,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
36 36
## UNC5D Expression
37 37
![image](images/gene_expression/UNC5D_by_pathology.svg)
38 38
39
-<!-- ORIGIN: NA -->
39
+<!-- ORIGIN: Unknown -->
USP7.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -42,4 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
42 42
43 43
## References
44 44
1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.*
45
-<!-- ORIGIN: NA -->
45
+<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
46
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
VMA21.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|FL |1 |high-confidence FL gene|
7
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/V
35 35
## VMA21 Expression
36 36
![image](images/gene_expression/VMA21_by_pathology.svg)
37 37
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
38
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
VPS13B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -41,4 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/V
41 41
![image](images/proteinpaint/VPS13B.svg)
42 42
## VPS13B Expression
43 43
![image](images/gene_expression/VPS13B_by_pathology.svg)
44
-<!-- ORIGIN: NA -->
44
+<!-- ORIGIN: Unknown -->
VWA7.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/V
37 37
## VWA7 Expression
38 38
![image](images/gene_expression/VWA7_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
WAC.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,4 +37,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
37 37
![image](images/proteinpaint/WAC.svg)
38 38
## WAC Expression
39 39
![image](images/gene_expression/WAC_by_pathology.svg)
40
-<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
40
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
42
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
WDFY3.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
38 38
## WDFY3 Expression
39 39
![image](images/gene_expression/WDFY3_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
WDR7.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
37 37
## WDR7 Expression
38 38
![image](images/gene_expression/WDR7_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
WDR90.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
37 37
## WDR90 Expression
38 38
![image](images/gene_expression/WDR90_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
WEE1.md
... ...
@@ -6,7 +6,7 @@ WEE1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -51,4 +51,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
51 51
![image](images/proteinpaint/WEE1.svg)
52 52
## WEE1 Expression
53 53
![image](images/gene_expression/WEE1_by_pathology.svg)
54
-<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
54
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
55
+<!-- PMBL: reichelFlowSortingExome2015a -->
56
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
WHAMM.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
37 37
## WHAMM Expression
38 38
![image](images/gene_expression/WHAMM_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
WNK1.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -52,4 +52,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
52 52
1. *Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L; ICGC MMML-Seq consortium; ICGC DE-Mining consortium; BLUEPRINT consortium; Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002-2016. doi: 10.1038/s41375-021-01251-z. Epub 2021 May 5. PMID: 33953289; PMCID: PMC8257491.*
53 53
2. *Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904-916. doi: 10.1182/blood.2022016534. PMID: 36201743; PMCID: PMC10023728.*
54 54
55
-<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
55
+<!-- ORIGIN: jalladesExomeSequencingIdentifies2017 -->
56
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
57
+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
58
+<!-- BL: thomasGeneticSubgroupsInform2023 -->
WNK2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
43 43
## WNK2 Expression
44 44
![image](images/gene_expression/WNK2_by_pathology.svg)
45 45
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
46
+<!-- BL: paneaWholeGenomeLandscape2019 -->
XBP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
XIRP2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/X
41 41
## XIRP2 Expression
42 42
![image](images/gene_expression/XIRP2_by_pathology.svg)
43 43
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
44
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
XPO1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -45,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/X
45 45
## XPO1 Expression
46 46
![image](images/gene_expression/XPO1_by_pathology.svg)
47 47
<!-- ORIGIN: mareschalWholeExomeSequencing2016 -->
48
+<!-- DLBCL: mareschalWholeExomeSequencing2016 -->
49
+<!-- PMBL: jardinRecurrentMutationsExportin2016a -->
YY1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Y
40 40
## YY1 Expression
41 41
![image](images/gene_expression/YY1_by_pathology.svg)
42 42
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
43
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
YY1AP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Y
37 37
## YY1AP1 Expression
38 38
![image](images/gene_expression/YY1AP1_by_pathology.svg)
39 39
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
ZAN.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -33,3 +33,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
33 33
## ZAN Expression
34 34
![image](images/gene_expression/ZAN_by_pathology.svg)
35 35
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
36
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
ZBTB7A.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -42,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
42 42
## ZBTB7A Expression
43 43
![image](images/gene_expression/ZBTB7A_by_pathology.svg)
44 44
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
45
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
46
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
ZC3H12A.md
... ...
@@ -4,8 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene |
8
-|FL |2 |relevance in FL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
9 9
10 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 11
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
## ZC3H12A Expression
38 38
![image](images/gene_expression/ZC3H12A_by_pathology.svg)
39 39
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
40
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
ZCCHC7.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -46,3 +46,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
46 46
## ZCCHC7 Expression
47 47
![image](images/gene_expression/ZCCHC7_by_pathology.svg)
48 48
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
49
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
ZEB2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
38 38
## ZEB2 Expression
39 39
![image](images/gene_expression/ZEB2_by_pathology.svg)
40 40
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
ZFAT.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
38 38
## ZFAT Expression
39 39
![image](images/gene_expression/ZFAT_by_pathology.svg)
40 40
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
ZFP36L1.md
... ...
@@ -6,8 +6,8 @@ ZFP36L1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
-|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
ZFX.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
41 41
## ZFX Expression
42 42
![image](images/gene_expression/ZFX_by_pathology.svg)
43 43
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
44
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
ZNF117.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
35 35
## ZNF117 Expression
36 36
![image](images/gene_expression/ZNF117_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
ZNF217.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,4 +37,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZNF217.svg)
38 38
## ZNF217 Expression
39 39
![image](images/gene_expression/ZNF217_by_pathology.svg)
40
-<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
40
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
41
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
42
+<!-- PMBL: reichelFlowSortingExome2015a -->
ZNF229.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
## ZNF229 Expression
38 38
![image](images/gene_expression/ZNF229_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
ZNF292.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
38 38
## ZNF292 Expression
39 39
![image](images/gene_expression/ZNF292_by_pathology.svg)
40 40
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
ZNF296.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
35 35
## ZNF296 Expression
36 36
![image](images/gene_expression/ZNF296_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38
+<!-- MCL: zhangGenomicLandscapeMantle2014 -->
ZNF423.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
38 38
## ZNF423 Expression
39 39
![image](images/gene_expression/ZNF423_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
ZNF608.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
38 38
## ZNF608 Expression
39 39
![image](images/gene_expression/ZNF608_by_pathology.svg)
40 40
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
42
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
ZNF85.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
## ZNF85 Expression
38 38
![image](images/gene_expression/ZNF85_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->