871b2056d3eb2dd4ed0ab89ce468286f4e351225
BCOR.md
| ... | ... | @@ -24,7 +24,7 @@ timeline |
| 24 | 24 | |:------:|:----:|--------------------------| |
| 25 | 25 | ||2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]| |
| 26 | 26 | | |2 |low-confidence DLBCL gene| |
| 27 | -| |1 |high-confidence MCL gene [@nadeuGenomicEpigenomicInsights2020b]| |
|
| 27 | +| |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 | -| |1-a | aSHM target and high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 25 | +| |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 | -||2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]| |
|
| 24 | -||1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]| |
|
| 23 | +||2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021]| |
|
| 24 | +||1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011]| |
|
| 25 | 25 | | |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]| |
| 26 | 26 | | |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 | -||1|high-confidence PMBL/cHL/GZL gene [@sarkozyMutationalLandscapeGray2021a]| |
|
| 26 | +||1|high-confidence PMBL/cHL/GZL gene [@sarkozyMutationalLandscapeGray2021]| |
|
| 27 | 27 | | |1 |high-confidence DLBCL gene [@reddyGeneticFunctionalDrivers2017; @arthurGenomewideDiscoverySomatic2018]| |
| 28 | 28 | | |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 | ||1|high-confidence MZL gene| |
| 30 | -| |1 |high-confidence DLBCL gene [@tiacciBRAFMutationsHairycell2011a]| |
|
| 30 | +| |1 |high-confidence DLBCL gene [@tiacciBRAFMutationsHairycell2011]| |
|
| 31 | 31 | | |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 | ||1|high-confidence MZL gene| |
| 39 | -||1|high-confidence PMBL/cHL/GZL gene[@sarkozyMutationalLandscapeGray2021a]| |
|
| 39 | +||1|high-confidence PMBL/cHL/GZL gene[@sarkozyMutationalLandscapeGray2021]| |
|
| 40 | 40 | | |1-EE[@mlynarczykBTG1MutationYields2023b; @delageBTG1InactivationDrives2023a] | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]| |
| 41 | 41 | | |1 | aSHM target and high-confidence FL gene | |
| 42 | -| |2 | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 42 | +| |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 | -||2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]| |
|
| 23 | +||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 | -| |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 22 | +| |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 | -||1|high-confidence MZL gene[@yanBCRTLRSignaling2012a]| |
|
| 36 | +||1|high-confidence MZL gene[@yanBCRTLRSignaling2012]| |
|
| 37 | 37 | | |1-EE |high-confidence DLBCL gene [@lenzOncogenicCARD11Mutations2008]| |
| 38 | 38 | | |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]| |
| 39 | 39 | | |1 |high-confidence MCL gene [@wuGeneticHeterogeneityPrimary2016]| |
CCL4.md
| ... | ... | @@ -18,7 +18,7 @@ timeline |
| 18 | 18 | |
| 19 | 19 | |Entity|Tier|Description | |
| 20 | 20 | |:------:|:----:|-----------------------------------------| |
| 21 | -| |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 21 | +| |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 | ||1|high-confidence MZL gene[@jalladesExomeSequencingIdentifies2017]| |
| 36 | 36 | ||2|relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]| |
| 37 | -| |1-EE |high-confidence BL gene [@richterRecurrentMutationID32012a]| |
|
| 37 | +| |1-EE |high-confidence BL gene [@richterRecurrentMutationID32012]| |
|
| 38 | 38 | | |1-EE |high-confidence DLBCL gene[@morinFrequentMutationHistonemodifying2011]| |
| 39 | 39 | | |1-EE |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]| |
| 40 | 40 |