CD58.md
... ...
@@ -33,7 +33,7 @@ timeline
33 33
34 34
|Entity|Tier|Description |
35 35
|:------:|:----:|--------------------------------------|
36
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@schneiderAlterationsCD58Gene2015a]|
36
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@schneiderAlterationsCD58Gene2015]|
37 37
|![DLBCL](images/icons/DLBCL_tier1.png) |1-EE |high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
38 38
39 39
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
DTX1.md
... ...
@@ -128,7 +128,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
128 128
**Rating**
129 129
★ ☆ ☆ ☆ ☆
130 130
131
-## DLBCL[@schmitzGeneticsPathogenesisDiffuse2018a]
131
+## DLBCL[@schmitzGeneticsPathogenesisDiffuse2018]
132 132
133 133
![](primary/Schmitz_113058428--DTX1--T_C--DLBCL11460T.pad100.png)
134 134
**Rating**
KLHL21.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|-----------------------------------------|
20
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@schmitzGeneticsPathogenesisDiffuse2018a]|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@schmitzGeneticsPathogenesisDiffuse2018]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
MAP2K1.md
... ...
@@ -19,7 +19,7 @@ timeline
19 19
|Entity|Tier|Description |
20 20
|:------:|:----:|-----------------------------------------|
21 21
|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@shinBRAFV600EMAP2K12015]|
22
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@louissaintPediatrictypeNodalFollicular2016a]|
22
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@louissaintPediatrictypeNodalFollicular2016]|
23 23
24 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 25
MAP3K14.md
... ...
@@ -21,8 +21,8 @@ timeline
21 21
22 22
|Entity|Tier|Description|
23 23
|:------:|:----:|--------------------------------------|
24
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]|
25
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@ottoGeneticLesionsTRAF32012a]|
24
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011]|
25
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@ottoGeneticLesionsTRAF32012]|
26 26
27 27
28 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MCRS1.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MFHAS1.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021a]|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MPDZ.md
... ...
@@ -18,7 +18,7 @@ timeline
18 18
19 19
|Entity|Tier|Description |
20 20
|:------:|:----:|-----------------------------------------|
21
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015a]|
21
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015]|
22 22
|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@morinMutationalStructuralAnalysis2013]|
23 23
24 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MSL2.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MYBPC2.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|-----------------------------------------|
20
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@schmitzGeneticsPathogenesisDiffuse2018a]|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@schmitzGeneticsPathogenesisDiffuse2018]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
MYD88.md
... ...
@@ -18,8 +18,8 @@ timeline
18 18
19 19
|Entity|Tier|Description |
20 20
|:------:|:----:|--------------------------------------|
21
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@yanBCRTLRSignaling2012a]|
22
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@ngoOncogenicallyActiveMYD882011a]|
21
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@yanBCRTLRSignaling2012]|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@ngoOncogenicallyActiveMYD882011]|
23 23
|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
24 24
25 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
N2RF2.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
23
+|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
TICRR.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015a]|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
TMSL3.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012a]|
23
+|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
TNF.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012a]|
23
+|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
TNFRSF14.md
... ...
@@ -24,9 +24,9 @@ timeline
24 24
25 25
|Entity|Tier|Description |
26 26
|:------:|:----:|--------------------------------------|
27
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@spinaGeneticsNodalMarginal2016b] |
27
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@spinaGeneticsNodalMarginal2016] |
28 28
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@morinFrequentMutationHistonemodifying2011] |
29
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@cheungAcquiredTNFRSF14Mutations2010a] |
29
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@cheungAcquiredTNFRSF14Mutations2010] |
30 30
31 31
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
32 32
TPP1.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|--------------------------------------|
20
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
20
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
TRAF6.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|-----------------------------------------|
20
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
TRRAP.md
... ...
@@ -19,7 +19,7 @@ timeline
19 19
20 20
|Entity|Tier|Description |
21 21
|:------:|:----:|--------------------------|
22
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
22
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012]|
23 23
|![DLBCL](images/icons/DLBCL_tier1.png) |3 |Retired for DLBCL[@zhangGeneticHeterogeneityDiffuse2013]|
24 24
25 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
UBE2A.md
... ...
@@ -24,7 +24,7 @@ timeline
24 24
25 25
|Entity|Tier|Description |
26 26
|:------:|:----:|--------------------------------------|
27
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
27
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015]|
28 28
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a; @albuquerqueEnhancingKnowledgeDiscovery2017a; @reddyGeneticFunctionalDrivers2017]|
29 29
30 30
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
UNC5B.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|-----------------------------------------|
20
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
UNC5C.md
... ...
@@ -18,7 +18,7 @@ timeline
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|--------------------------|
20 20
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |2 |low-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
21
+|![DLBCL](images/icons/DLBCL_tier1.png) |2 |low-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012]|
22 22
23 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
24 24
VPS13B.md
... ...
@@ -10,7 +10,7 @@ link-citations: true
10 10
|Entity|Tier|Description |
11 11
|:------:|:----:|--------------------------|
12 12
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
13
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012]|
14 14
15 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
16 16
VWA7.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
WDR87.md
... ...
@@ -20,7 +20,7 @@ timeline
20 20
21 21
|Entity|Tier|Description|
22 22
|:------:|:----:|--------------------------------------|
23
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021]|
24 24
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
WEE1.md
... ...
@@ -21,8 +21,8 @@ timeline
21 21
22 22
|Entity|Tier|Description |
23 23
|:------:|:----:|--------------------------|
24
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
25
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene[@schmitzGeneticsPathogenesisDiffuse2018a]|
24
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015]|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene[@schmitzGeneticsPathogenesisDiffuse2018]|
26 26
27 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
28 28
WNK1.md
... ...
@@ -21,7 +21,7 @@ timeline
21 21
|:------:|:----:|-----------------------------------------|
22 22
|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
23 23
|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene [@thomasGeneticSubgroupsInform2023]|
24
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
24
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021]|
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27 27
XIRP2.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|--------------------------------------|
20
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023b]|
20
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
XPO1.md
... ...
@@ -22,7 +22,7 @@ timeline
22 22
23 23
|Entity|Tier|Description |
24 24
|:------:|:----:|--------------------------|
25
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@jardinRecurrentMutationsExportin2016a]|
25
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@jardinRecurrentMutationsExportin2016]|
26 26
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@mareschalWholeExomeSequencing2016; @reddyGeneticFunctionalDrivers2017]|
27 27
28 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
ZAN.md
... ...
@@ -17,7 +17,7 @@ timeline
17 17
18 18
|Entity|Tier|Description |
19 19
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022]|
21 21
22 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 23
ZFP36L1.md
... ...
@@ -28,7 +28,7 @@ timeline
28 28
|Entity|Tier|Description |
29 29
|:------:|:----:|--------------------------------------|
30 30
|![MCL](images/icons/MCL_tier2.png)|2|relevance in MCL not firmly established|
31
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
31
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015]|
32 32
|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@paneaWholeGenomeLandscape2019]|
33 33
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
34 34