ACAD9.md
... ...
@@ -15,6 +15,8 @@ Due to [minimal support](ACAD9#representative-mutation) in the original primary
15 15
|:------:|:----:|--------------------------------------|
16 16
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |3 |Retired, Failed QC[@reddyGeneticFunctionalDrivers2017]|
18 15
|![MCL](images/icons/MCL_tier2.png) |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
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@gomezUltraDeepSequencingReveals2023]|
17 15
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@tiacciBRAFMutationsHairycell2011]|
21 22
|![BL](images/icons/Tier2_BL.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier1.png) |1 | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
20 21
|![FL](images/icons/FL_tier1.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established [@loveGeneticLandscapeMutations2012]|
18 18
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |3 |Retired, Failed QC [@reddyGeneticFunctionalDrivers2017]|
17 15
|![BL](images/icons/BL_tier1.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier1.png) |1 | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
24 23
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
25 21
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
21 19
|![FL](images/icons/FL_tier1.png) |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
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017]|
22 21
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]|
21 21
|![DLBCL](images/icons/DLBCL_tier1.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
16 15
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@tiacciPervasiveMutationsJAKSTAT2018]|
16 15
|![BL](images/icons/BL_tier2.png) |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
|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019]|
19 19
|![DLBCL](images/icons/DLBCL_tier1.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]|
21 20
|![DLBCL](images/icons/DLBCL_tier1.png) |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
|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]|
16 15
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019]|
16 15
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
21 21
|![MCL](images/icons/MCL_tier1.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |3 |Retired, Failed QC[@paneaWholeGenomeLandscape2019]|
21 18
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]|
16 15
|![MCL](images/icons/MCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@tiacciPervasiveMutationsJAKSTAT2018]|
14 14
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |3 |Retired, Failed QC[@loveGeneticLandscapeMutations2012]|
16 15
|![DLBCL](images/icons/DLBCL_tier1.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012]|
16 15
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established [@burkhardtClinicalRelevanceMolecular2022]|
17 16
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![DLBCL](images/icons/DLBCL_tier2.png) |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
|![BL](images/icons/BL_tier2.png) |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 (%)|