0b1d04665c3f3f76284d5e63757ffadfd31ddcf9
ACAD9.md
| ... | ... | @@ -15,6 +15,8 @@ Due to [minimal support](ACAD9#representative-mutation) in the original primary |
| 15 | 15 | |:------:|:----:|--------------------------------------| |
| 16 | 16 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 18 | 20 | <<Warn("The variants reported in this gene in BL failed QC")>> |
| 19 | 21 | |
| 20 | 22 |
ACE.md
| ... | ... | @@ -9,7 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Due to [minimal support](ACE#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 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 13 | 12 | |
| 14 | 13 | |
| 15 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -18,6 +17,10 @@ Due to [minimal support](ACE#representative-mutation) in the original primary da |
| 18 | 17 | |:------:|:----:|--------------------------------------| |
| 19 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 23 | + |
|
| 21 | 24 | |
| 22 | 25 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 23 | 26 |
ALPK2.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,11 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 19 | + |
|
| 20 | + |
|
| 17 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 22 | |
| 19 | 23 | |Entity|source |frequency (%)| |
ARID1B.md
| ... | ... | @@ -6,9 +6,6 @@ link-citations: true |
| 6 | 6 | |
| 7 | 7 | [[_TOC_]] |
| 8 | 8 | |
| 9 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 10 | - |
|
| 11 | - |
|
| 12 | 9 | |
| 13 | 10 | ## Relevance tier by entity |
| 14 | 11 | |
| ... | ... | @@ -17,6 +14,11 @@ link-citations: true |
| 17 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 18 | 15 | | |2 |relevance in MCL not firmly established | |
| 19 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 21 | + |
|
| 20 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 21 | 23 | |
| 22 | 24 | |Entity|source |frequency (%)| |
ARID5B.md
| ... | ... | @@ -6,8 +6,6 @@ link-citations: true |
| 6 | 6 | |
| 7 | 7 | [[_TOC_]] |
| 8 | 8 | |
| 9 | -<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>> |
|
| 10 | - |
|
| 11 | 9 | |
| 12 | 10 | ## Relevance tier by entity |
| 13 | 11 | |
| ... | ... | @@ -16,6 +14,11 @@ link-citations: true |
| 16 | 14 | ||1|high-confidence PMBL/cHL/GZL gene[@gomezUltraDeepSequencingReveals2023]| |
| 17 | 15 | | |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017;@drevalRevisitingReddyDLBCL2023; @arthurGenomewideDiscoverySomatic2018]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>> |
|
| 20 | + |
|
| 21 | + |
|
| 19 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 23 | |
| 21 | 24 | |Entity|source |frequency (%)| |
ATP2C2.md
| ... | ... | @@ -7,9 +7,9 @@ link-citations: true |
| 7 | 7 | |
| 8 | 8 | |
| 9 | 9 | ## Overview |
| 10 | + |
|
| 10 | 11 | Due to [minimal support](ATP2C2#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 | 12 | |
| 12 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 13 | 13 | |
| 14 | 14 | |
| 15 | 15 | ## Relevance tier by entity |
| ... | ... | @@ -18,6 +18,11 @@ Due to [minimal support](ATP2C2#representative-mutation) in the original primary |
| 18 | 18 | |:------:|:----:|--------------------------------------| |
| 19 | 19 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 20 | |
| 21 | +## Warnings |
|
| 22 | + |
|
| 23 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 24 | + |
|
| 25 | + |
|
| 21 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 27 | |
| 23 | 28 | |Entity|source |frequency (%)| |
BRAF.md
| ... | ... | @@ -5,9 +5,10 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | ## Overview |
| 11 | + |
|
| 11 | 12 | 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] |
| 12 | 13 | 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. |
| 13 | 14 | |
| ... | ... | @@ -20,6 +21,11 @@ Although mutations have also been reported in BL, due to [minimal support](BRAF# |
| 20 | 21 | | |1 |high-confidence DLBCL gene [@tiacciBRAFMutationsHairycell2011]| |
| 21 | 22 | | |2 |Failed QC[@loveGeneticLandscapeMutations2012]| |
| 22 | 23 | |
| 24 | +## Warnings |
|
| 25 | + |
|
| 26 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 27 | + |
|
| 28 | + |
|
| 23 | 29 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 30 | |
| 25 | 31 | [[include:DLBCL_BRAF.md]] |
BRD4.md
| ... | ... | @@ -9,8 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Due to [minimal support](BRD4#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 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 13 | - |
|
| 14 | 12 | |
| 15 | 13 | ## Relevance tier by entity |
| 16 | 14 | |
| ... | ... | @@ -18,6 +16,11 @@ Due to [minimal support](BRD4#representative-mutation) in the original primary d |
| 18 | 16 | |:------:|:----:|--------------------------------------| |
| 19 | 17 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 22 | + |
|
| 23 | + |
|
| 21 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 25 | |
| 23 | 26 | |Entity|source |frequency (%)| |
BTG2.md
| ... | ... | @@ -5,9 +5,10 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | ## Overview |
| 11 | + |
|
| 11 | 12 | BTG2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. Mutations in the BTG2 gene have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL), contributing to the development and progression of the disease. These mutations are a feature of the MCD genetic subgroup of DLBCL. The biological function of BTG2 mutations and their role in lymphomagenesis remains poorly understood. Due to [minimal support](BTG2#representative-mutations) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| 12 | 13 | |
| 13 | 14 | |
| ... | ... | @@ -19,6 +20,11 @@ BTG2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 19 | 20 | | |1 | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]| |
| 20 | 21 | | |1 | aSHM target and high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]| |
| 21 | 22 | |
| 23 | +## Warnings |
|
| 24 | + |
|
| 25 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 26 | + |
|
| 27 | + |
|
| 22 | 28 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 23 | 29 | |
| 24 | 30 | [[include:DLBCL_BTG2.md]] |
C6orf27.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | ## Overview |
| 11 | 10 | |
| ... | ... | @@ -18,6 +17,11 @@ Due to [minimal support](C6orf27#representative-mutation) in the original primar |
| 18 | 17 | |:------:|:----:|--------------------------------------| |
| 19 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 24 | + |
|
| 21 | 25 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 26 | |
| 23 | 27 | |Entity|source |frequency (%)| |
CAD.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | ## Overview |
| 11 | 10 | |
| ... | ... | @@ -18,6 +17,10 @@ Due to [minimal support](CAD#representative-mutation) in the original primary da |
| 18 | 17 | |:------:|:----:|--------------------------------------| |
| 19 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 21 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 25 | |
| 23 | 26 | |Entity|source |frequency (%)| |
CBLB.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 8 | +## Overview |
|
| 9 | 9 | |
| 10 | 10 | 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. |
| 11 | 11 | |
| ... | ... | @@ -16,6 +16,9 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup |
| 16 | 16 | |:------:|:----:|-----------------------------------------| |
| 17 | 17 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 18 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | 22 | |
| 20 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 21 | 24 |
CCT6B.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | ## Overview |
| 11 | 11 | |
| ... | ... | @@ -18,6 +18,10 @@ Due to [minimal support](CCT6B#representative-mutations) in the original primary |
| 18 | 18 | |:------:|:----:|--------------------------------------| |
| 19 | 19 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 20 | |
| 21 | +## Warnings |
|
| 22 | + |
|
| 23 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 24 | + |
|
| 21 | 25 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 26 | |
| 23 | 27 | |Entity|source |frequency (%)| |
CDC73.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 8 | +## Overview |
|
| 9 | 9 | |
| 10 | 10 | Mutations in this gene were first described in BL in 2012 by Love et al<sup>1</sup> and subsequently in DLBCL by Reddy et al.<sup>2</sup> Subsequent exome and genome-wide studies of DLBCL and BL did not reproduce these observations. |
| 11 | 11 | |
| ... | ... | @@ -17,6 +17,10 @@ Mutations in this gene were first described in BL in 2012 by Love et al<sup>1</s |
| 17 | 17 | | |2 |relevance in BL not firmly established [@loveGeneticLandscapeMutations2012]| |
| 18 | 18 | | |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]| |
| 19 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 23 | + |
|
| 20 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 21 | 25 | |
| 22 | 26 | |Entity|source |frequency (%)| |
CDH17.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | ## Overview |
| 11 | 10 | |
| ... | ... | @@ -18,6 +17,10 @@ Due to [minimal support](CDH17#representative-mutations) in the original primary |
| 18 | 17 | |:------:|:----:|--------------------------------------| |
| 19 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 21 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 25 | |
| 23 | 26 | |Entity|source |frequency (%)| |
CHD1.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 8 | +## Overview |
|
| 9 | 9 | |
| 10 | 10 | 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. |
| 11 | 11 | |
| ... | ... | @@ -16,6 +16,10 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup |
| 16 | 16 | |:------:|:----:|-----------------------------------------| |
| 17 | 17 | | |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]| |
| 18 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
CHD8.md
| ... | ... | @@ -5,8 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | - |
|
| 10 | 8 | |
| 11 | 9 | ## Relevance tier by entity |
| 12 | 10 | |
| ... | ... | @@ -16,6 +14,10 @@ link-citations: true |
| 16 | 14 | | |3 |Retired, Failed QC [@reddyGeneticFunctionalDrivers2017]| |
| 17 | 15 | | |1 |high-confidence BL gene [@grandeGenomewideDiscoverySomatic2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 19 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 22 | |
| 21 | 23 | [[include:DLBCL_CHD8.md]] |
CHST2.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 8 | +## Overview |
|
| 9 | 9 | |
| 10 | 10 | 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. |
| 11 | 11 | |
| ... | ... | @@ -16,6 +16,10 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup |
| 16 | 16 | |:------:|:----:|-----------------------------------------| |
| 17 | 17 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 18 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
COL4A2.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | ## Overview |
| 11 | 11 | |
| ... | ... | @@ -19,6 +19,10 @@ Due to [minimal support](COL4A2#representative-mutations) in the original primar |
| 19 | 19 | |:------:|:----:|--------------------------------------| |
| 20 | 20 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 21 | 21 | |
| 22 | +## Warnings |
|
| 23 | + |
|
| 24 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 25 | + |
|
| 22 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 23 | 27 | |
| 24 | 28 | |Entity|source |frequency (%)| |
CTCF.md
| ... | ... | @@ -5,8 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | - |
|
| 10 | 8 | |
| 11 | 9 | |
| 12 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +13,10 @@ link-citations: true |
| 15 | 13 | |:------:|:----:|--------------------------------------| |
| 16 | 14 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 17 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 19 | + |
|
| 18 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 21 | |
| 20 | 22 | |Entity|source |frequency (%)| |
CYB5D1.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | |
| ... | ... | @@ -15,6 +15,10 @@ link-citations: true |
| 15 | 15 | |:------:|:----:|--------------------------------------| |
| 16 | 16 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 21 | + |
|
| 18 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 23 | |
| 20 | 24 | |Entity|source |frequency (%)| |
CYP4F22.md
| ... | ... | @@ -9,8 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Due to [minimal support](CYP4F22#representative-mutation) in the original primary data, [low expression in BL](CYP4F22#cyp4f22-expression) and no mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| 11 | 11 | |
| 12 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 13 | - |
|
| 14 | 12 | |
| 15 | 13 | |
| 16 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -19,6 +17,10 @@ Due to [minimal support](CYP4F22#representative-mutation) in the original primar |
| 19 | 17 | |:------:|:----:|--------------------------------------| |
| 20 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 21 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 22 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 23 | 25 | |
| 24 | 26 | |Entity|source |frequency (%)| |
DCAF6.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 8 | +## Overview |
|
| 9 | 9 | |
| 10 | 10 | 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. |
| 11 | 11 | |
| ... | ... | @@ -16,6 +16,10 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup |
| 16 | 16 | |:------:|:----:|-----------------------------------------| |
| 17 | 17 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 18 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
DLGAP1.md
| ... | ... | @@ -9,9 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Due to [minimal support](DLGAP1#representative-mutation) in the original primary data, [low expression in BL](DLGAP1#dlgap1-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| 11 | 11 | |
| 12 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 13 | - |
|
| 14 | - |
|
| 15 | 12 | |
| 16 | 13 | ## Relevance tier by entity |
| 17 | 14 | |
| ... | ... | @@ -19,6 +16,10 @@ Due to [minimal support](DLGAP1#representative-mutation) in the original primary |
| 19 | 16 | |:------:|:----:|--------------------------------------| |
| 20 | 17 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 21 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 22 | + |
|
| 22 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 23 | 24 | |
| 24 | 25 | |Entity|source |frequency (%)| |
DNMT1.md
| ... | ... | @@ -5,9 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | - |
|
| 10 | - |
|
| 11 | 8 | |
| 12 | 9 | ## Relevance tier by entity |
| 13 | 10 | |
| ... | ... | @@ -15,6 +12,10 @@ link-citations: true |
| 15 | 12 | |:------:|:----:|--------------------------------------| |
| 16 | 13 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 17 | 14 | |
| 15 | +## Warnings |
|
| 16 | + |
|
| 17 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 18 | + |
|
| 18 | 19 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 20 | |
| 20 | 21 | |Entity|source |frequency (%)| |
DNMT3A.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | |
| ... | ... | @@ -15,6 +15,10 @@ link-citations: true |
| 15 | 15 | |:------:|:----:|-----------------------------------------| |
| 16 | 16 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 17 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 21 | + |
|
| 18 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 23 | |
| 20 | 24 | |Entity|source |frequency (%)| |
EIF2C4.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | |
| ... | ... | @@ -15,6 +15,10 @@ link-citations: true |
| 15 | 15 | |:------:|:----:|--------------------------------------| |
| 16 | 16 | | |2 | Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 21 | + |
|
| 18 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 23 | |
| 20 | 24 | |Entity|source |frequency (%)| |
EML2.md
| ... | ... | @@ -5,9 +5,11 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | +## Overview |
|
| 9 | + |
|
| 8 | 10 | Due to [minimal support](EML2#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. |
| 9 | 11 | |
| 10 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 12 | + |
|
| 11 | 13 | |
| 12 | 14 | |
| 13 | 15 | |
| ... | ... | @@ -17,6 +19,10 @@ Due to [minimal support](EML2#representative-mutation) in the original primary d |
| 17 | 19 | |:------:|:----:|--------------------------------------| |
| 18 | 20 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 19 | 21 | |
| 22 | +## Warnings |
|
| 23 | + |
|
| 24 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 25 | + |
|
| 20 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 21 | 27 | |
| 22 | 28 | |Entity|source |frequency (%)| |
ENTPD3.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | |
| ... | ... | @@ -15,6 +15,10 @@ link-citations: true |
| 15 | 15 | |:------:|:----:|--------------------------------------| |
| 16 | 16 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 21 | + |
|
| 18 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 23 | |
| 20 | 24 | |Entity|source |frequency (%)| |
EPHB2.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | |
| ... | ... | @@ -16,6 +16,10 @@ link-citations: true |
| 16 | 16 | |:------:|:----:|--------------------------------------| |
| 17 | 17 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 18 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
ETS1.md
| ... | ... | @@ -11,7 +11,6 @@ ETS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) |
| 11 | 11 | This gene has some recurrent sites of mutations (hot spots). |
| 12 | 12 | The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*. |
| 13 | 13 | |
| 14 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 15 | 14 | |
| 16 | 15 | |
| 17 | 16 | |
| ... | ... | @@ -23,6 +22,10 @@ The mutation pattern in DLBCL implies the preferential accumulation of *inactiva |
| 23 | 22 | | |1 | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]| |
| 24 | 23 | | |3 | Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 25 | 24 | |
| 25 | +## Warnings |
|
| 26 | + |
|
| 27 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 28 | + |
|
| 26 | 29 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 27 | 30 | |
| 28 | 31 | [[include:DLBCL_ETS1.md]] |
FAM129B.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | |
| ... | ... | @@ -15,6 +15,10 @@ link-citations: true |
| 15 | 15 | |:------:|:----:|--------------------------------------| |
| 16 | 16 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 21 | + |
|
| 18 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 23 | |
| 20 | 24 | |Entity|source |frequency (%)| |
FGFR3.md
| ... | ... | @@ -9,7 +9,7 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Due to [minimal support](FGFR3#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 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 12 | + |
|
| 13 | 13 | |
| 14 | 14 | |
| 15 | 15 | ## Relevance tier by entity |
| ... | ... | @@ -18,6 +18,10 @@ Due to [minimal support](FGFR3#representative-mutation) in the original primary |
| 18 | 18 | |:------:|:----:|--------------------------------------| |
| 19 | 19 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 20 | |
| 21 | +## Warnings |
|
| 22 | + |
|
| 23 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 24 | + |
|
| 21 | 25 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 26 | |
| 23 | 27 | |Entity|source |frequency (%)| |
FTCD.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | ## Overview |
| ... | ... | @@ -21,6 +21,10 @@ Due to [minimal support](FTCD#representative-mutation) in the original primary d |
| 21 | 21 | |:------:|:----:|--------------------------------------| |
| 22 | 22 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 23 | 23 | |
| 24 | +## Warnings |
|
| 25 | + |
|
| 26 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 27 | + |
|
| 24 | 28 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 25 | 29 | |
| 26 | 30 | |Entity|source |frequency (%)| |
FZD3.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in BL in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,11 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in BL in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 19 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 23 | |
| 21 | 24 | |Entity|source |frequency (%)| |
GNAS.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
GRIK5.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
HIST1H1C.md
| ... | ... | @@ -9,10 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | This is one of several genes that encode linker histone proteins that are recurrently mutated in DLBCL and FL.<sup>1,2</sup> Mutations are often found in the globular domain of the protein, which is critical for its interaction with DNA and other histone proteins. |
| 11 | 11 | |
| 12 | -<<Warn("The variants reported in BL in this gene failed QC")>> |
|
| 13 | - |
|
| 14 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 15 | - |
|
| 16 | 12 | |
| 17 | 13 | |
| 18 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -24,6 +20,12 @@ This is one of several genes that encode linker histone proteins that are recurr |
| 24 | 20 | | |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]| |
| 25 | 21 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]]| |
| 26 | 22 | |
| 23 | +## Warnings |
|
| 24 | + |
|
| 25 | +<<Warn("The variants reported in BL in this gene failed QC")>> |
|
| 26 | + |
|
| 27 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 28 | + |
|
| 27 | 29 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 28 | 30 | |
| 29 | 31 | ### DLBCL |
HIST1H2AG.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in BL in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | |
| ... | ... | @@ -20,6 +18,12 @@ link-citations: true |
| 20 | 18 | | |2 |relevance in DLBCL not firmly established| |
| 21 | 19 | | |1 |high-confidence FL gene | |
| 22 | 20 | |
| 21 | +## Warnings |
|
| 22 | + |
|
| 23 | +<<Warn("The variants reported in BL in this gene failed QC")>> |
|
| 24 | + |
|
| 25 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 26 | + |
|
| 23 | 27 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 28 | |
| 25 | 29 | |Entity|source |frequency (%)| |
HIST1H2AM.md
| ... | ... | @@ -5,11 +5,10 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | ## Overview |
| 11 | + |
|
| 13 | 12 | This gene encodes the H2A protein, one of the core proteins comprising nucleosomes. Although relatively common in DLBCL, little is known about the function of these mutations. |
| 14 | 13 | |
| 15 | 14 | |
| ... | ... | @@ -21,6 +20,12 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom |
| 21 | 20 | | |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017]| |
| 22 | 21 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 23 | 22 | |
| 23 | +## Warnings |
|
| 24 | + |
|
| 25 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 26 | + |
|
| 27 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 28 | + |
|
| 24 | 29 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 25 | 30 | |
| 26 | 31 | ### DLBCL |
HIST1H2BK.md
| ... | ... | @@ -9,7 +9,7 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | This gene encodes the H2A protein, one of the core proteins comprising nucleosomes. Although relatively common in DLBCL, little is known about the function of these mutations. |
| 11 | 11 | |
| 12 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 12 | + |
|
| 13 | 13 | |
| 14 | 14 | |
| 15 | 15 | ## Relevance tier by entity |
| ... | ... | @@ -20,6 +20,10 @@ This gene encodes the H2A protein, one of the core proteins comprising nucleosom |
| 20 | 20 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 21 | 21 | | |1 |high-confidence DLBCL gene [@zhangGeneticHeterogeneityDiffuse2013; @chapuyMolecularSubtypesDiffuse2018]| |
| 22 | 22 | |
| 23 | +## Warnings |
|
| 24 | + |
|
| 25 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 26 | + |
|
| 23 | 27 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 28 | |
| 25 | 29 | ### DLBCL |
HIST1H3H.md
| ... | ... | @@ -5,9 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | - |
|
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 8 | |
| 12 | 9 | |
| 13 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +13,12 @@ link-citations: true |
| 16 | 13 | |:------:|:----:|--------------------------------------| |
| 17 | 14 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 20 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 21 | + |
|
| 19 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 23 | |
| 21 | 24 | |Entity|source |frequency (%)| |
HIST1H3J.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | |
| ... | ... | @@ -17,6 +15,12 @@ link-citations: true |
| 17 | 15 | |:------:|:----:|--------------------------------------| |
| 18 | 16 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 19 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 21 | + |
|
| 22 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 23 | + |
|
| 20 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 21 | 25 | |
| 22 | 26 | |Entity|source |frequency (%)| |
HRAS.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | ||2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]| |
| 16 | 15 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
ICK.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## arnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
ITPR3.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | ||2|relevance in PMBL/cHL/GZL not firmly established[@tiacciPervasiveMutationsJAKSTAT2018]| |
| 16 | 15 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
JUNB.md
| ... | ... | @@ -5,7 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1)")>> |
|
| 8 | + |
|
| 9 | 9 | |
| 10 | 10 | ## Overview |
| 11 | 11 | JUNB has been reported to be frequently mutated in T-cell/histiocyte-rich large B-cell lymphoma (THRLBCL).<sup>[@schuhmacherJUNBDUSP2SGK12019]</sup> Mutations have also been reported in DLBCL but the mutation rate in the earliest study<sup>[@reddyGeneticFunctionalDrivers2017]</sup> was likely an over-estimate.<sup>[@drevalRevisitingReddyDLBCL2023]</sup> According to one study, mutations are often enriched at somatic hypermutation hotspot sites, indicating the involvement of aberrant somatic hypermutation in the pathogenesis of these lymphomas.<sup>[@schuhmacherJUNBDUSP2SGK12019]</sup> |
| ... | ... | @@ -18,6 +18,12 @@ JUNB has been reported to be frequently mutated in T-cell/histiocyte-rich large |
| 18 | 18 | ||2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019]| |
| 19 | 19 | | |1 |high-confidence DLBCL gene[@reddyGeneticFunctionalDrivers2017; @hubschmannMutationalMechanismsShaping2021]| |
| 20 | 20 | |
| 21 | +## Warnings |
|
| 22 | + |
|
| 23 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 24 | + |
|
| 25 | +Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
|
| 26 | + |
|
| 21 | 27 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 28 | |
| 23 | 29 | [[include:DLBCL_JUNB.md]] |
KCNK10.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
KIFC3.md
| ... | ... | @@ -5,9 +5,9 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | +## Overview |
|
| 8 | 9 | Due to [minimal support](KIFC3#representative-mutations) in the original primary data, [low expression in BL](KIFC3#kifc3-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| 9 | 10 | |
| 10 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 11 | 11 | |
| 12 | 12 | |
| 13 | 13 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +16,10 @@ Due to [minimal support](KIFC3#representative-mutations) in the original primary |
| 16 | 16 | |:------:|:----:|--------------------------------------| |
| 17 | 17 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 18 | 18 | |
| 19 | +## Warnings |
|
| 20 | + |
|
| 21 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
LIN54.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
MAP3K6.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
MAP4K4.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
MARK1.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | |:------:|:----:|-----------------------------------------| |
| 16 | 15 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
MME.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
MSH2.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
MTOR.md
| ... | ... | @@ -9,7 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Although mutations in MTOR have been reported in DLBCL and some BL, their role in lymphomagenesis has not been thoroughly studied. |
| 11 | 11 | |
| 12 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 13 | 12 | |
| 14 | 13 | |
| 15 | 14 | |
| ... | ... | @@ -20,6 +19,10 @@ Although mutations in MTOR have been reported in DLBCL and some BL, their role i |
| 20 | 19 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 21 | 20 | | |1 |high-confidence DLBCL gene[@zhangGeneticHeterogeneityDiffuse2013; @reddyGeneticFunctionalDrivers2017] | |
| 22 | 21 | |
| 22 | +## Warnings |
|
| 23 | + |
|
| 24 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 25 | + |
|
| 23 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 27 | |
| 25 | 28 | [[include:DLBCL_MTOR.md]] |
MYB.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | ||2|relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]| |
| 16 | 15 | | |3 |Retired, Failed QC| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
MYH10.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
NCOR1.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
NFKB2.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | ||2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019]| |
| 16 | 15 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
NOTCH1.md
| ... | ... | @@ -6,8 +6,8 @@ link-citations: true |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | 8 | ## Overview |
| 9 | + |
|
| 9 | 10 | The relevance of NOTCH1 mutations in various malignancies has been well established. However, *due to [minimal support](NOTCH1#representative-mutations) in the original primary data and very few mutations reported in subsequent BL studies, this gene is very unlikely to be relevant in BL.* |
| 10 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 11 | 11 | |
| 12 | 12 | |
| 13 | 13 | |
| ... | ... | @@ -20,6 +20,10 @@ The relevance of NOTCH1 mutations in various malignancies has been well establis |
| 20 | 20 | | |1 |high-confidence DLBCL gene | |
| 21 | 21 | | |1 |high-confidence MCL gene | |
| 22 | 22 | |
| 23 | +## Warnings |
|
| 24 | + |
|
| 25 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 26 | + |
|
| 23 | 27 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 28 | |
| 25 | 29 | [[include:DLBCL_NOTCH1.md]] |
NRXN2.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
PABPC4L.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
PC.md
| ... | ... | @@ -6,8 +6,7 @@ link-citations: true |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | 8 | |
| 9 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 10 | -Due to [minimal support](PC#representative-mutations) in the original primary data, [low expression in BL](PC#pc-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
|
| 9 | + |
|
| 11 | 10 | |
| 12 | 11 | ## Relevance tier by entity |
| 13 | 12 | |
| ... | ... | @@ -15,6 +14,11 @@ Due to [minimal support](PC#representative-mutations) in the original primary da |
| 15 | 14 | |:------:|:----:|--------------------------------------| |
| 16 | 15 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 20 | +Due to [minimal support](PC#representative-mutations) in the original primary data, [low expression in BL](PC#pc-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
|
| 21 | + |
|
| 18 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 23 | |
| 20 | 24 | |Entity|source |frequency (%)| |
PCDHA11.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
PDZRN3.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
PIK3R1.md
| ... | ... | @@ -5,12 +5,9 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -Mutations in this gene were first described in DLBCL in 2013[@zhangGeneticHeterogeneityDiffuse2013] and by the same group in a subsequent study.[@reddyGeneticFunctionalDrivers2017] It remains in Tier 2 because other exome and genome-wide studies of DLBCL did not reproduce this observation. |
|
| 9 | - |
|
| 10 | - |
|
| 11 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 8 | +## Overview |
|
| 12 | 9 | |
| 13 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 10 | +Mutations in this gene were first described in DLBCL in 2013[@zhangGeneticHeterogeneityDiffuse2013] and by the same group in a subsequent study.[@reddyGeneticFunctionalDrivers2017] It remains in Tier 2 because other exome and genome-wide studies of DLBCL did not reproduce this observation. |
|
| 14 | 11 | |
| 15 | 12 | |
| 16 | 13 | ## Relevance tier by entity |
| ... | ... | @@ -20,6 +17,12 @@ Mutations in this gene were first described in DLBCL in 2013[@zhangGeneticHetero |
| 20 | 17 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 21 | 18 | | |2 |relevance in DLBCL not firmly established[@zhangGeneticHeterogeneityDiffuse2013]| |
| 22 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 23 | + |
|
| 24 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 25 | + |
|
| 23 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 27 | |
| 25 | 28 | |Entity|source |frequency (%)| |
POLRMT.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
POR.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 | Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
PRSS22.md
| ... | ... | @@ -9,7 +9,6 @@ link-citations: true |
| 9 | 9 | |
| 10 | 10 | Due to [minimal support](PRSS22#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 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 13 | 12 | |
| 14 | 13 | |
| 15 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -18,6 +17,10 @@ Due to [minimal support](PRSS22#representative-mutation) in the original primary |
| 18 | 17 | |:------:|:----:|--------------------------------------| |
| 19 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 20 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 23 | + |
|
| 21 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 25 | |
| 23 | 26 | |Entity|source |frequency (%)| |
PTPRK.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
PTPRN.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
PXDNL.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
RARA.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
RBP3.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
RET.md
| ... | ... | @@ -5,9 +5,10 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | +## Overview |
|
| 9 | + |
|
| 8 | 10 | Due to [minimal support](RET#representative-mutation) in the original primary data, [low expression in BL](RET#ret-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| 9 | 11 | |
| 10 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 11 | 12 | |
| 12 | 13 | |
| 13 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +17,10 @@ Due to [minimal support](RET#representative-mutation) in the original primary da |
| 16 | 17 | |:------:|:----:|--------------------------------------| |
| 17 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 18 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 19 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 25 | |
| 21 | 26 | |Entity|source |frequency (%)| |
RUNX1.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
SALL3.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | | |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
SAPS2.md
| ... | ... | @@ -6,7 +6,6 @@ link-citations: true |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | 8 | |
| 9 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 10 | 9 | |
| 11 | 10 | |
| 12 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | |:------:|:----:|--------------------------------------| |
| 16 | 15 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
SETD5.md
| ... | ... | @@ -13,6 +13,8 @@ link-citations: true |
| 13 | 13 | ||2|relevance in PMBL/cHL/GZL not firmly established[@tiacciPervasiveMutationsJAKSTAT2018]| |
| 14 | 14 | | |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]| |
| 15 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 16 | 18 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| 17 | 19 | |
| 18 | 20 | Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
SF3B1.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | | |1 |high-confidence DLBCL gene [@reddyGeneticFunctionalDrivers2017; @chapuyMolecularSubtypesDiffuse2018] | |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in BL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | [[include:DLBCL_SF3B1.md]] |
SHANK1.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3|Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
SLC29A2.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3| Retired, Failed QC [@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
SNTB2.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
SYK.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
SYNGAP1.md
| ... | ... | @@ -5,9 +5,10 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | +## Overview |
|
| 9 | + |
|
| 8 | 10 | Due to [minimal support](SYNGAP1#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. |
| 9 | 11 | |
| 10 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 11 | 12 | |
| 12 | 13 | |
| 13 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +17,10 @@ Due to [minimal support](SYNGAP1#representative-mutation) in the original primar |
| 16 | 17 | |:------:|:----:|--------------------------------------| |
| 17 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 18 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 19 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 25 | |
| 21 | 26 | |Entity|source |frequency (%)| |
TBC1D9B.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
TIGD6.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3|Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
TPST2.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|--------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
WAC.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -15,6 +14,10 @@ link-citations: true |
| 15 | 14 | ||2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012]| |
| 16 | 15 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 17 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 20 | + |
|
| 18 | 21 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 22 | |
| 20 | 23 | |Entity|source |frequency (%)| |
WDR7.md
| ... | ... | @@ -5,9 +5,7 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 9 | 8 | |
| 10 | -**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 11 | 9 | |
| 12 | 10 | |
| 13 | 11 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +14,12 @@ link-citations: true |
| 16 | 14 | |:------:|:----:|--------------------------------------| |
| 17 | 15 | | |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]| |
| 18 | 16 | |
| 17 | +## Warnings |
|
| 18 | + |
|
| 19 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 20 | + |
|
| 21 | +**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information** |
|
| 22 | + |
|
| 19 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 24 | |
| 21 | 25 | |Entity|source |frequency (%)| |
YY1.md
| ... | ... | @@ -12,6 +12,8 @@ link-citations: true |
| 12 | 12 | |:------:|:----:|-----------------------------------------| |
| 13 | 13 | | |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017; @chapuyMolecularSubtypesDiffuse2018]| |
| 14 | 14 | |
| 15 | +## Warnings |
|
| 16 | + |
|
| 15 | 17 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| 16 | 18 | |
| 17 | 19 | Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
ZBTB7A.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | |
| ... | ... | @@ -16,6 +15,10 @@ link-citations: true |
| 16 | 15 | | |2 |relevance in BL not firmly established [@burkhardtClinicalRelevanceMolecular2022]| |
| 17 | 16 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 18 | 17 | |
| 18 | +## Warnings |
|
| 19 | + |
|
| 20 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 21 | + |
|
| 19 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 23 | |
| 21 | 24 | |Entity|source |frequency (%)| |
ZFAT.md
| ... | ... | @@ -5,7 +5,6 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | -<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 9 | 8 | |
| 10 | 9 | |
| 11 | 10 | ## Relevance tier by entity |
| ... | ... | @@ -14,6 +13,10 @@ link-citations: true |
| 14 | 13 | |:------:|:----:|-----------------------------------------| |
| 15 | 14 | | |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]| |
| 16 | 15 | |
| 16 | +## Warnings |
|
| 17 | + |
|
| 18 | +<<Warn("The variants reported in this gene in DLBCL failed QC")>> |
|
| 19 | + |
|
| 17 | 20 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 21 | |
| 19 | 22 | |Entity|source |frequency (%)| |
ZFX.md
| ... | ... | @@ -12,6 +12,8 @@ link-citations: true |
| 12 | 12 | |:------:|:----:|-----------------------------------------| |
| 13 | 13 | | |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]| |
| 14 | 14 | |
| 15 | +## Warnings |
|
| 16 | + |
|
| 15 | 17 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| 16 | 18 | |
| 17 | 19 | Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
ZNF229.md
| ... | ... | @@ -5,9 +5,10 @@ link-citations: true |
| 5 | 5 | --- |
| 6 | 6 | [[_TOC_]] |
| 7 | 7 | |
| 8 | +## Overview |
|
| 9 | + |
|
| 8 | 10 | Due to [minimal support](ZNF229#representative-mutation) in the original primary data, [low expression in BL](ZNF229#znf229-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| 9 | 11 | |
| 10 | -<<Warn("The variants reported in this gene failed QC")>> |
|
| 11 | 12 | |
| 12 | 13 | |
| 13 | 14 | ## Relevance tier by entity |
| ... | ... | @@ -16,6 +17,10 @@ Due to [minimal support](ZNF229#representative-mutation) in the original primary |
| 16 | 17 | |:------:|:----:|--------------------------------------| |
| 17 | 18 | | |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]| |
| 18 | 19 | |
| 20 | +## Warnings |
|
| 21 | + |
|
| 22 | +<<Warn("The variants reported in this gene failed QC")>> |
|
| 23 | + |
|
| 19 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 25 | |
| 21 | 26 | |Entity|source |frequency (%)| |