BCOR.md
... ...
@@ -24,7 +24,7 @@ timeline
24 24
|:------:|:----:|--------------------------|
25 25
|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
26 26
|![DLBCL](images/icons/DLBCL_tier1.png) |2 |low-confidence DLBCL gene|
27
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@nadeuGenomicEpigenomicInsights2020b]|
27
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@nadeuGenomicEpigenomicInsights2020]|
28 28
29 29
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
30 30
BCR.md
... ...
@@ -22,7 +22,7 @@ timeline
22 22
23 23
|Entity|Tier|Description |
24 24
|:------:|:----:|--------------------------------------|
25
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a]|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012]|
26 26
27 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
28 28
BIRC3.md
... ...
@@ -20,8 +20,8 @@ timeline
20 20
21 21
|Entity|Tier|Description |
22 22
|:------:|:----:|-----------------------------------------|
23
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]|
24
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021]|
24
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011]|
25 25
|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]|
26 26
|![MCL](images/icons/MCL_tier1.png) |1-a | aSHM target and high-confidence MCL gene [@beaLandscapeSomaticMutations2013]|
27 27
BIRC6.md
... ...
@@ -23,7 +23,7 @@ timeline
23 23
24 24
|Entity|Tier|Description |
25 25
|:------:|:----:|--------------------------------------|
26
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene [@sarkozyMutationalLandscapeGray2021a]|
26
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene [@sarkozyMutationalLandscapeGray2021]|
27 27
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@reddyGeneticFunctionalDrivers2017; @arthurGenomewideDiscoverySomatic2018]|
28 28
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
29 29
BRAF.md
... ...
@@ -6,7 +6,7 @@ link-citations: true
6 6
# BRAF
7 7
8 8
## Overview
9
-BRAF mutations, particularly the BRAF V600E hot spot mutation, are primarily associated with hairy cell leukemia and are rare in other B-cell lymphomas. These mutations play a crucial role in the pathogenesis of HCL and have important diagnostic and therapeutic implications. Although they are rare, mutations in BRAF are reproducibly observed in some DLBCLs. Another hot spot, D594A, occurs in DLBCL. The role of these in lymphomagenesis remains poorly understood but functional evidence suggests they may contribute to aneuploidy.[@tiacciBRAFMutationsHairycell2011a]
9
+BRAF mutations, particularly the BRAF V600E hot spot mutation, are primarily associated with hairy cell leukemia and are rare in other B-cell lymphomas. These mutations play a crucial role in the pathogenesis of HCL and have important diagnostic and therapeutic implications. Although they are rare, mutations in BRAF are reproducibly observed in some DLBCLs. Another hot spot, D594A, occurs in DLBCL. The role of these in lymphomagenesis remains poorly understood but functional evidence suggests they may contribute to aneuploidy.[@tiacciBRAFMutationsHairycell2011]
10 10
Although mutations have also been reported in BL, due to [minimal support](BRAF#representative-mutation) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL.
11 11
12 12
<<Warn("The variants reported in this gene in BL failed QC")>>
... ...
@@ -27,7 +27,7 @@ timeline
27 27
|Entity|Tier|Description |
28 28
|:------:|:----:|--------------------------------------|
29 29
|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
30
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@tiacciBRAFMutationsHairycell2011a]|
30
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@tiacciBRAFMutationsHairycell2011]|
31 31
|![BL](images/icons/Tier2_BL.png) |2 |Failed QC[@loveGeneticLandscapeMutations2012]|
32 32
33 33
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
BTG1.md
... ...
@@ -13,8 +13,8 @@ These mutations are a feature of the MCD genetic subgroup of DLBCL.
13 13
14 14
## Experimental Evidence
15 15
16
-Mutations in the BTG1 gene have been implicated in the pathogenesis and progression of diffuse large B-cell lymphoma (DLBCL) through functional exploration in vivo. Knock-out of BTG1 did not lead to spontaneous lymphomagenesis but enhanced the lymphoproliferation induced by VavP-BCL2 and promoted lymphoma dissemination in xenotransplantation experiments.[@delageBTG1InactivationDrives2023a]
17
-Another study demonstrated that specific BTG1 mutations afford germinal center (GC) B cells with a fitness advantage relative to un-mutated counterparts.[@mlynarczykBTG1MutationYields2023b]
16
+Mutations in the BTG1 gene have been implicated in the pathogenesis and progression of diffuse large B-cell lymphoma (DLBCL) through functional exploration in vivo. Knock-out of BTG1 did not lead to spontaneous lymphomagenesis but enhanced the lymphoproliferation induced by VavP-BCL2 and promoted lymphoma dissemination in xenotransplantation experiments.[@delageBTG1InactivationDrives2023]
17
+Another study demonstrated that specific BTG1 mutations afford germinal center (GC) B cells with a fitness advantage relative to un-mutated counterparts.[@mlynarczykBTG1MutationYields2023]
18 18
19 19
```mermaid
20 20
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -36,10 +36,10 @@ timeline
36 36
|Entity|Tier|Description |
37 37
|:------:|:----:|--------------------------------------|
38 38
|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
39
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@sarkozyMutationalLandscapeGray2021a]|
39
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@sarkozyMutationalLandscapeGray2021]|
40 40
|![DLBCL](images/icons/DLBCL_tier1.png) |1-EE[@mlynarczykBTG1MutationYields2023b; @delageBTG1InactivationDrives2023a] | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
41 41
|![FL](images/icons/FL_tier1.png) |1 | aSHM target and high-confidence FL gene |
42
-|![BL](images/icons/BL_tier2.png) |2 | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@burkhardtClinicalRelevanceMolecular2022b]|
42
+|![BL](images/icons/BL_tier2.png) |2 | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@burkhardtClinicalRelevanceMolecular2022]|
43 43
44 44
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
45 45
C6orf103.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
CADPS2.md
... ...
@@ -19,7 +19,7 @@ timeline
19 19
20 20
|Entity|Tier|Description |
21 21
|:------:|:----:|-----------------------------------------|
22
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021]|
23 23
24 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 25
CARD11.md
... ...
@@ -33,7 +33,7 @@ timeline
33 33
34 34
|Entity|Tier|Description |
35 35
|:------:|:----:|--------------------------------------|
36
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@yanBCRTLRSignaling2012a]|
36
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@yanBCRTLRSignaling2012]|
37 37
|![DLBCL](images/icons/DLBCL_tier1.png) |1-EE |high-confidence DLBCL gene [@lenzOncogenicCARD11Mutations2008]|
38 38
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
39 39
|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@wuGeneticHeterogeneityPrimary2016]|
CCL4.md
... ...
@@ -18,7 +18,7 @@ timeline
18 18
19 19
|Entity|Tier|Description |
20 20
|:------:|:----:|-----------------------------------------|
21
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]|
21
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018]|
22 22
23 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
24 24
CCND3.md
... ...
@@ -34,7 +34,7 @@ timeline
34 34
|:------:|:----:|--------------------------|
35 35
|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@jalladesExomeSequencingIdentifies2017]|
36 36
|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]|
37
-|![BL](images/icons/BL_tier1.png) |1-EE |high-confidence BL gene [@richterRecurrentMutationID32012a]|
37
+|![BL](images/icons/BL_tier1.png) |1-EE |high-confidence BL gene [@richterRecurrentMutationID32012]|
38 38
|![DLBCL](images/icons/DLBCL_tier1.png) |1-EE |high-confidence DLBCL gene[@morinFrequentMutationHistonemodifying2011]|
39 39
|![FL](images/icons/FL_tier1.png) |1-EE |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
40 40