ABL2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ACAD9.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ACE.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ACTB.md
... ...
@@ -7,8 +7,8 @@ ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------|
10
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
11
-|FL |1-a |high-confidence FL gene, hypermutated |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated|
11
+|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated |
12 12
13 13
14 14
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
ADAMTS1.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et a
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|-----------------------------------------|
10
-|DLBCL |2 |relevance in DLBCL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
ADAMTS5.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ADNP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
AGO4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
AICDA.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ALPK2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ANK2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ANKRD12.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et a
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|-----------------------------------------|
10
-|DLBCL |2 |relevance in DLBCL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
ARHGEF1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ARID1A.md
... ...
@@ -10,9 +10,9 @@ ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes
10 10
11 11
|Entity|Tier|Description |
12 12
|:------:|:----:|--------------------------|
13
-|BL |1 |high-confidence BL gene |
14
-|DLBCL |1 |high-confidence DLBCL gene|
15
-|FL |1 |high-confidence FL gene |
13
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
14
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
15
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
16 16
## Mutation incidence in large cohorts
17 17
18 18
|Entity|source |frequency (%)|
ATP11C.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7
-|MCL |2 |relevance in MCL not firmly established|
7
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ATP2C2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ATP6AP1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|FL |1 |high-confidence FL gene|
7
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
ATP6V1A.md
... ...
@@ -7,7 +7,7 @@ Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et a
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------------------|
10
-|FL |2 |relevance in FL not firmly established|
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
11 11
12 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 13
ATP6V1B2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7
-|FL |1 |high-confidence FL gene|
7
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
Audit-of-B\342\200\220cell-Cancer-Genes.md
... ...
@@ -2,3 +2,4 @@
2 2
This is a community-driven resource and knowledge base initiated by members of the Lymphoma/Leukemia Molecular Profiling Project and fuelled by results from the genomic analysis of mature B-cell lymphomas (GAMBL) project. ## ATR Expression
3 3
![image](images/gene_expression/ATR_by_pathology.svg)
4 4
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
5
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
BTG1.md
... ...
@@ -86,3 +86,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
86 86
3. *Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science. 2023 Jan 20;379(6629):eabj7412. doi: 10.1126/science.abj7412. Epub 2023 Jan 20. PMID: 36656933; PMCID: PMC10515739.*
87 87
4. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
88 88
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
89
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
90
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
91
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
BTG2.md
... ...
@@ -57,3 +57,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
57 57
2. *Guo D, Hong L, Ji H, Jiang Y, Lu L, Wang X, Huang H. The Mutation of BTG2 Gene Predicts a Poor Outcome in Primary Testicular Diffuse Large B-Cell Lymphoma. J Inflamm Res. 2022 Mar 10;15:1757-1769. doi: 10.2147/JIR.S341355. PMID: 35300216; PMCID: PMC8923029.*
58 58
3. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
59 59
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
60
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
61
+<!-- BL: loveGeneticLandscapeMutations2012 -->
62
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
BTK.md
... ...
@@ -42,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
42 42
## BTK Expression
43 43
![image](images/gene_expression/BTK_by_pathology.svg)
44 44
<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
45
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
46
+<!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a -->
C6orf27.md
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
31 31
## C6orf27 Expression
32 32
![image](images/gene_expression/C6orf27_by_pathology.svg)
33 33
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34
+<!-- BL: loveGeneticLandscapeMutations2012 -->
CAD.md
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43 43
## CAD Expression
44 44
![image](images/gene_expression/CAD_by_pathology.svg)
45 45
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
46
+<!-- BL: loveGeneticLandscapeMutations2012 -->
CADPS2.md
... ...
@@ -1,5 +1,8 @@
1 1
# CADPS2
2 2
3
+## History
4
+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -24,10 +27,6 @@
24 27
|FL |No |No |0.921 |0.000 |
25 28
26 29
27
-> [!NOTE]
28
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
29
-
30
-
31 30
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CADPS2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CADPS2_protein_hg38.html)
32 31
33 32
![image](images/proteinpaint/CADPS2_NM_017954.svg)
... ...
@@ -37,4 +36,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 36
![image](images/proteinpaint/CADPS2.svg)
38 37
## CADPS2 Expression
39 38
![image](images/gene_expression/CADPS2_by_pathology.svg)
39
+
40
+## References
41
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
42
+
43
+
40 44
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
45
+
46
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
CARD11.md
... ...
@@ -1,13 +1,14 @@
1 1
# CARD11
2 2
3
+
3 4
## Relevance tier by entity
4 5
5 6
|Entity|Tier|Description |
6 7
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |1 |high-confidence FL gene |
10
-|MCL |1 |high-confidence MCL gene |
8
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
11
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
11 12
12 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 14
... ...
@@ -68,3 +69,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
68 69
## CARD11 Expression
69 70
![image](images/gene_expression/CARD11_by_pathology.svg)
70 71
<!-- ORIGIN: lenzOncogenicCARD11Mutations2008 -->
72
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
73
+<!-- MCL: wuGeneticHeterogeneityPrimary2016 -->
74
+<!-- MZL: yanBCRTLRSignaling2012a -->
75
+<!-- DLBCL: lenzOncogenicCARD11Mutations2008 -->
CARD4.md
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
31 31
## CARD4 Expression
32 32
![image](images/gene_expression/CARD4_by_pathology.svg)
33 33
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34
+<!-- BL: loveGeneticLandscapeMutations2012 -->
CBLB.md
... ...
@@ -1,10 +1,12 @@
1 1
# CBLB
2
+## History
3
+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.
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 10
9 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
... ...
@@ -24,10 +26,6 @@
24 26
|FL |No |No |0.000 |0 |
25 27
26 28
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29
-
30
-
31 29
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CBLB_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CBLB_protein_hg38.html)
32 30
33 31
![image](images/proteinpaint/CBLB_NM_170662.svg)
... ...
@@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 35
![image](images/proteinpaint/CBLB.svg)
38 36
## CBLB Expression
39 37
![image](images/gene_expression/CBLB_by_pathology.svg)
38
+
39
+## References
40
+1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
41
+
40 42
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
43
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CCDC42BPB.md
... ...
@@ -1,5 +1,8 @@
1 1
# CCDC42BPB
2 2
3
+## History
4
+Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -26,6 +29,13 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
26 29
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_hg38.html)
27 30
28 31
![image](images/proteinpaint/CCDC42BPB.svg)
32
+
29 33
## CCDC42BPB Expression
30 34
![image](images/gene_expression/CCDC42BPB_by_pathology.svg)
35
+
36
+## References
37
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
38
+
39
+
31 40
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
41
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
CCL4.md
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 38
## CCL4 Expression
39 39
![image](images/gene_expression/CCL4_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
CCND1.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7
-|MCL |1 |high-confidence MCL gene|
7
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
35 35
## CCND1 Expression
36 36
![image](images/gene_expression/CCND1_by_pathology.svg)
37 37
<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
38
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
CCND3.md
... ...
@@ -6,9 +6,9 @@ CCND3 (Cyclin D3) is a gene that encodes a protein involved in the regulation of
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|BL |1 |high-confidence BL gene |
10
-|DLBCL |1 |high-confidence DLBCL gene|
11
-|FL |1 |high-confidence FL gene |
9
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
11
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 12
13 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 14
... ...
@@ -91,3 +91,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
91 91
## CCND3 Expression
92 92
![image](images/gene_expression/CCND3_by_pathology.svg)
93 93
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
94
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
95
+<!-- BL: richterRecurrentMutationID32012a -->
96
+<!-- BL: richterRecurrentMutationID32012a -->
97
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
98
+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
CCNF.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
## CCNF Expression
38 38
![image](images/gene_expression/CCNF_by_pathology.svg)
39 39
<!-- ORIGIN: abateDistinctViralMutational2015a -->
40
+<!-- BL: abateDistinctViralMutational2015a -->
CCT6B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
## CCT6B Expression
38 38
![image](images/gene_expression/CCT6B_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
CD22.md
... ...
@@ -1,10 +1,12 @@
1 1
# CD22
2
+## History
3
+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.
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 10
9 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
... ...
@@ -24,10 +26,6 @@
24 26
|FL |No |No |0.000 |0 |
25 27
26 28
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29
-
30
-
31 29
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD22_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD22_protein_hg38.html)
32 30
33 31
![image](images/proteinpaint/CD22_NM_001771.svg)
... ...
@@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 35
![image](images/proteinpaint/CD22.svg)
38 36
## CD22 Expression
39 37
![image](images/gene_expression/CD22_by_pathology.svg)
38
+
39
+## References
40
+1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
41
+
40 42
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
43
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CD274.md
... ...
@@ -6,7 +6,7 @@ the CD274 gene encodes the programmed death-ligand 1 (PD-L1). Mutations in B-cel
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -47,3 +47,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
47 47
1. *Huang RSP, Decker B, Murugesan K, Hiemenz M, Mata DA, Li G, Creeden J, Ramkissoon SH, Ross JS. Pan-cancer analysis of CD274 (PD-L1) mutations in 314,631 patient samples and subset correlation with PD-L1 protein expression. J Immunother Cancer. 2021 Jun;9(6):e002558. doi: 10.1136/jitc-2021-002558. PMID: 34130989; PMCID: PMC8207995.*
48 48
2. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
49 49
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
50
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
CD36.md
... ...
@@ -6,7 +6,7 @@ CD36 is a transmembrane glycoprotein involved in fatty acid metabolism, glucose
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 10
11 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 12
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
44 44
## CD36 Expression
45 45
![image](images/gene_expression/CD36_by_pathology.svg)
46 46
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
47
+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
CD44.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43 43
## CD44 Expression
44 44
![image](images/gene_expression/CD44_by_pathology.svg)
45 45
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
CD58.md
... ...
@@ -7,8 +7,7 @@ CD58, also known as lymphocyte function-associated antigen 3 (LFA-3), is crucial
7 7
8 8
|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------------------|
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|BL |2 |relevance in BL not firmly established|
10
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
CD70.md
... ...
@@ -6,9 +6,8 @@ CD70 is a costimulatory molecule expressed on some activated lymphocytes and has
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |2 |relevance in FL not firmly established|
11
-|BL |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
12 11
13 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 13
... ...
@@ -57,3 +56,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
57 56
## CD70 Expression
58 57
![image](images/gene_expression/CD70_by_pathology.svg)
59 58
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
59
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
60
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
CD79A.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -43,4 +43,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43 43
![image](images/proteinpaint/CD79A.svg)
44 44
## CD79A Expression
45 45
![image](images/gene_expression/CD79A_by_pathology.svg)
46
-<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
46
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
47
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
48
+<!-- MZL: rossiCodingGenomeSplenic2012c -->
CD83.md
... ...
@@ -3,6 +3,10 @@
3 3
4 4
CD83 is a transmembrane protein that plays a role in the immune system, particularly in the maturation and function of dendritic cells, T cells, and B cells with a role in regulating immune responses and maintaining immune tolerance.<sup>1</sup> CD83 mutations in B-cell lymphomas have not been as extensively studied as mutations in some other genes. CD83 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. No notable hot spots have been described in this gene in the context of the cancers listed below.
5 5
6
+## History
7
+Mutations in this gene were first described in DLBCL in 2013 by Morin et al<sup>2</sup>, in BL in 2019 by Panea et al<sup>3</sup> and in FL in 2023 by Russler-Germain et al.<sup>4</sup>
8
+
9
+
6 10
## Relevance tier by entity
7 11
8 12
|Entity|Tier|Description |
... ...
@@ -56,5 +60,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
56 60
## References
57 61
1. *Lechmann M, Zinser E, Golka A, Steinkasserer A. Role of CD83 in the immunomodulation of dendritic cells. Int Arch Allergy Immunol. 2002 Oct;129(2):113-8. doi: 10.1159/000065883. PMID: 12403928.*
58 62
2. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
59
-3. *Russler-Germain DA, Krysiak K, Ramirez C, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen AF, Mehta-Shah N, Kahl BS, Bartlett NL, Alderuccio JP, Lossos IS, Ondrejka SL, Hsi ED, Martin P, Leonard JP, Griffith M, Griffith OL, Fehniger TA. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Adv. 2023 Sep 26;7(18):5524-5539. doi: 10.1182/bloodadvances.2023010779. PMID: 37493986; PMCID: PMC10514406.*
63
+3. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
64
+4. *Russler-Germain DA, Krysiak K, Ramirez C, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen AF, Mehta-Shah N, Kahl BS, Bartlett NL, Alderuccio JP, Lossos IS, Ondrejka SL, Hsi ED, Martin P, Leonard JP, Griffith M, Griffith OL, Fehniger TA. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Adv. 2023 Sep 26;7(18):5524-5539. doi: 10.1182/bloodadvances.2023010779. PMID: 37493986; PMCID: PMC10514406.*
60 65
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
66
+<!-- BL: paneaWholeGenomeLandscape2019 -->
67
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
68
+<!-- BL: paneaWholeGenomeLandscape2019 -->
69
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
CDC73.md
... ...
@@ -1,11 +1,13 @@
1 1
# CDC73
2
+## History
3
+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.
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
10
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 11
10 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 13
... ...
@@ -27,11 +29,6 @@
27 29
|DLBCL |No |No |1.702 |0 |
28 30
|FL |No |No |3.603 |0 |
29 31
30
-
31
-> [!NOTE]
32
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
33
-
34
-
35 32
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDC73_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDC73_protein_hg38.html)
36 33
37 34
![image](images/proteinpaint/CDC73_NM_024529.svg)
... ...
@@ -39,6 +36,16 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
39 36
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDC73.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDC73_hg38.html)
40 37
41 38
![image](images/proteinpaint/CDC73.svg)
39
+
42 40
## CDC73 Expression
43 41
![image](images/gene_expression/CDC73_by_pathology.svg)
42
+
43
+## References
44
+1. *Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561*
45
+
46
+2. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
47
+
48
+
44 49
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
50
+<!-- BL: loveGeneticLandscapeMutations2012 -->
51
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CDH9.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 38
## CDH9 Expression
39 39
![image](images/gene_expression/CDH9_by_pathology.svg)
40 40
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
CDKN2A.md
... ...
@@ -2,12 +2,16 @@
2 2
## Overview
3 3
Although CDKN2A aberrations are common in DLBCL, this gene is predominantly affected by copy number alterations. One study found that deletions of the CDKN2A locus occur in about one-third of DLBCL patients.<sup>1</sup> The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. This gene has some recurrent sites of mutations (hotspots) with the most common mutation causing a truncation at codon 80 (R80*).
4 4
5
+## History
6
+Mutations in this gene were first described in DLBCL and FL in 2013 by Morin et al<sup>2</sup> and in BL in 2019 by Grande et al.<sup>3</sup>
7
+
8
+
5 9
## Relevance tier by entity
6 10
7 11
|Entity|Tier|Description |
8 12
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|BL |2 |relevance in BL not firmly established|
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
14
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
11 15
12 16
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 17
... ...
@@ -53,4 +57,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
53 57
## References
54 58
1. *Guney S, Jardin F, Bertrand P, Mareschal S, Parmentier F, Picquenot JM, Tilly H, Bastard C. Several mechanisms lead to the inactivation of the CDKN2A (P16), P14ARF, or CDKN2B (P15) genes in the GCB and ABC molecular DLBCL subtypes. Genes Chromosomes Cancer. 2012 Sep;51(9):858-67. doi: 10.1002/gcc.21970. Epub 2012 May 23. PMID: 22619049.*
55 59
56
-<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
60
+2. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992*
61
+
62
+3. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
63
+
64
+
65
+<!-- ORIGIN: 23699601 -->
66
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
67
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
68
+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
CDKN2C.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
## CDKN2C Expression
38 38
![image](images/gene_expression/CDKN2C_by_pathology.svg)
39 39
<!-- ORIGIN: thomasGeneticSubgroupsInform2023 -->
40
+<!-- BL: thomasGeneticSubgroupsInform2023 -->
CHD1.md
... ...
@@ -1,10 +1,12 @@
1 1
# CHD1
2
+## History
3
+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.
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 10
9 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
... ...
@@ -24,10 +26,6 @@
24 26
|FL |No |No |0.000 |0.000 |
25 27
26 28
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29
-
30
-
31 29
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD1_protein_hg38.html)
32 30
33 31
![image](images/proteinpaint/CHD1_NM_001270.svg)
... ...
@@ -35,6 +33,13 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
35 33
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD1_hg38.html)
36 34
37 35
![image](images/proteinpaint/CHD1.svg)
36
+
38 37
## CHD1 Expression
39 38
![image](images/gene_expression/CHD1_by_pathology.svg)
39
+
40
+## References
41
+1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
42
+
43
+
40 44
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
45
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CHD4.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
## CHD4 Expression
38 38
![image](images/gene_expression/CHD4_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
CILP.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
7
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
35 35
## CILP Expression
36 36
![image](images/gene_expression/CILP_by_pathology.svg)
37 37
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38
+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
CNOT2.md
... ...
@@ -1,5 +1,8 @@
1 1
# CNOT2
2 2
3
+## History
4
+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -23,11 +26,6 @@
23 26
|DLBCL |No |No |5.016 |12.509 |
24 27
|FL |No |No |0.000 |23.991 |
25 28
26
-
27
-> [!NOTE]
28
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
29
-
30
-
31 29
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNOT2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNOT2_protein_hg38.html)
32 30
33 31
![image](images/proteinpaint/CNOT2_NM_014515.svg)
... ...
@@ -35,6 +33,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
35 33
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNOT2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNOT2_hg38.html)
36 34
37 35
![image](images/proteinpaint/CNOT2.svg)
36
+
38 37
## CNOT2 Expression
39 38
![image](images/gene_expression/CNOT2_by_pathology.svg)
39
+
40
+## References
41
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
42
+
40 43
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
44
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
CNTNAP5.md
... ...
@@ -1,4 +1,6 @@
1 1
# CNTNAP5
2
+## History
3
+Mutations in this gene were first described in DLBCL in 2013 by Morin et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
... ...
@@ -24,10 +26,6 @@
24 26
|FL |No |No |2.893 |0.000 |
25 27
26 28
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29
-
30
-
31 29
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNTNAP5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNTNAP5_protein_hg38.html)
32 30
33 31
![image](images/proteinpaint/CNTNAP5_NM_130773.svg)
... ...
@@ -37,4 +35,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 35
![image](images/proteinpaint/CNTNAP5.svg)
38 36
## CNTNAP5 Expression
39 37
![image](images/gene_expression/CNTNAP5_by_pathology.svg)
38
+
39
+## References
40
+1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992
41
+
42
+
40 43
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
44
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
COL4A2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
## COL4A2 Expression
38 38
![image](images/gene_expression/COL4A2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
COQ7.md
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 38
## COQ7 Expression
39 39
![image](images/gene_expression/COQ7_by_pathology.svg)
40 40
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
DHX15.md
... ...
@@ -1,4 +1,6 @@
1 1
# DHX15
2
+## History
3
+Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
... ...
@@ -34,4 +36,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
34 36
![image](images/proteinpaint/DHX15.svg)
35 37
## DHX15 Expression
36 38
![image](images/gene_expression/DHX15_by_pathology.svg)
39
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
40
+
41
+
37 42
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
43
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
DHX16.md
... ...
@@ -1,4 +1,6 @@
1 1
# DHX16
2
+## History
3
+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
... ...
@@ -37,4 +39,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
37 39
![image](images/proteinpaint/DHX16.svg)
38 40
## DHX16 Expression
39 41
![image](images/gene_expression/DHX16_by_pathology.svg)
42
+
43
+## References
44
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
45
+
40 46
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
47
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
DNM2.md
... ...
@@ -1,4 +1,6 @@
1 1
# DNM2
2
+## History
3
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
... ...
@@ -24,10 +26,6 @@
24 26
|FL |No |No |10.522 |0.000 |
25 27
26 28
27
-> [!NOTE]
28
-
29
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
30
-
31 29
## DNM2 Hotspots
32 30
33 31
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -43,4 +41,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
43 41
![image](images/proteinpaint/DNM2.svg)
44 42
## DNM2 Expression
45 43
![image](images/gene_expression/DNM2_by_pathology.svg)
44
+
45
+## References
46
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
47
+
48
+
46 49
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
50
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
EEF1A1.md
... ...
@@ -2,6 +2,10 @@
2 2
## Overview
3 3
Mutations in the EEF1A1 gene, which encodes the eukaryotic translation elongation factor 1A1, have been reported in DLBCL and FL.<sup>1</sup> This gene has some recurrent sites of mutations (hot spots). The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. Paradoxically, one study showed that EEF1A1 knock down reduced proliferation in vitro and in xenograft experiments.<sup>2</sup>
4 4
5
+## History
6
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
7
+
8
+
5 9
## Relevance tier by entity
6 10
7 11
|Entity|Tier|Description |
... ...
@@ -55,4 +59,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
55 59
2. *Gong T, Shuang Y. Expression and Clinical Value of Eukaryotic Translation Elongation Factor 1A1 (EEF1A1) in Diffuse Large B Cell Lymphoma. Int J Gen Med. 2021 Oct 27;14:7247-7258. doi: 10.2147/IJGM.S324645. PMID: 34737619; PMCID: PMC8559353.*
56 60
## EEF1A1 Expression
57 61
![image](images/gene_expression/EEF1A1_by_pathology.svg)
58
-<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
62
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
63
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
64
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
65
+<!-- PMBL: reichelFlowSortingExome2015a -->
FOXP1.md
... ...
@@ -1,10 +1,11 @@
1 1
# FOXP1
2 2
3
+
3 4
## Relevance tier by entity
4 5
5 6
|Entity|Tier|Description |
6 7
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 9
9 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
FZD3.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
37 37
## FZD3 Expression
38 38
![image](images/gene_expression/FZD3_by_pathology.svg)
39 39
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40
+<!-- BL: paneaWholeGenomeLandscape2019 -->
GNAI2.md
... ...
@@ -2,13 +2,16 @@
2 2
## Overview
3 3
Mutations in the GNAI2 gene, which encodes the G protein alpha subunit involved in signal transduction, have been identified as significant contributors to the pathogenesis of B-cell lymphomas, including BL, DLBCL and, to a lesser extent, FL.<sup>1</sup> Mutations in GNAI2, along with GNA13 and other small GTPases, affect the signaling pathways that regulate B-cell homing. These mutations are thought to cause aberrant localization and function of B-cells within lymphoid tissues.<sup>1</sup> The functional role of these mutations has not been studied as extensively as those in GNA13 and further work is needed to elucidate the specific role of these mutations in lymphomagenesis.
4 4
5
+## History
6
+Mutations were first described in DLBCL in 2013 by Morin et al<sup>1</sup> and in BL in 2019 by Grande et al.<sup>2</sup>
7
+
5 8
## Relevance tier by entity
6 9
7 10
|Entity|Tier|Description |
8 11
|:------:|:----:|--------------------------|
9
-|BL |1 |high-confidence BL gene |
10
-|DLBCL |1 |high-confidence DLBCL gene|
11
-|FL |1 |high-confidence FL gene |
12
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
14
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
12 15
13 16
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 17
... ...
@@ -32,10 +35,6 @@ Mutations in the GNAI2 gene, which encodes the G protein alpha subunit involved
32 35
|FL |No |Yes |55.205 | 0.000 |
33 36
34 37
35
-> [!NOTE]
36
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
37
-
38
-
39 38
## GNAI2 Hotspots
40 39
41 40
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -60,8 +59,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
60 59
61 60
![image](images/proteinpaint/GNAI2.svg)
62 61
63
-## References
64
-1. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
65 62
## GNAI2 Expression
66 63
![image](images/gene_expression/GNAI2_by_pathology.svg)
64
+
65
+## References
66
+1. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992*
67
+
68
+2. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
69
+
67 70
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
71
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
72
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
HIST1H1C.md
... ...
@@ -2,13 +2,17 @@
2 2
## Overview
3 3
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.
4 4
5
+## History
6
+Mutations in this gene were first described in DLBCL and FL in 2011 by Morin et al.<sup>1</sup> Mutations were subsequently reported in BL by Panea et al.<sup>3</sup>
7
+
8
+
5 9
## Relevance tier by entity
6 10
7 11
|Entity|Tier|Description |
8 12
|:------:|:----:|--------------------------------------|
9
-|BL |2 |relevance in BL not firmly established|
10
-|DLBCL |1 |high-confidence DLBCL gene |
11
-|FL |1 |high-confidence FL gene |
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
14
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
15
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
12 16
13 17
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 18
... ...
@@ -32,10 +36,6 @@ This is one of several genes that encode linker histone proteins that are recurr
32 36
|FL |No |No | 4.446 |0 |
33 37
34 38
35
-> [!NOTE]
36
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
37
-
38
-
39 39
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HIST1H1C_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HIST1H1C_protein_hg38.html)
40 40
41 41
![image](images/proteinpaint/HIST1H1C_NM_005319.svg)
... ...
@@ -44,10 +44,18 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
44 44
45 45
![image](images/proteinpaint/HIST1H1C.svg)
46 46
47
+
48
+## HIST1H1C Expression
49
+![image](images/gene_expression/HIST1H1C_by_pathology.svg)
50
+
47 51
## References
48 52
49 53
1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
50 54
2. *Li H, Kaminski MS, Li Y, Yildiz M, Ouillette P, Jones S, Fox H, Jacobi K, Saiya-Cork K, Bixby D, Lebovic D, Roulston D, Shedden K, Sabel M, Marentette L, Cimmino V, Chang AE, Malek SN. Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. Blood. 2014 Mar 6;123(10):1487-98. doi: 10.1182/blood-2013-05-500264. Epub 2014 Jan 16. PMID: 24435047; PMCID: PMC4729540.*
51
-## HIST1H1C Expression
52
-![image](images/gene_expression/HIST1H1C_by_pathology.svg)
55
+3. *Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;*
56
+
57
+
53 58
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
59
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
60
+<!-- BL: paneaWholeGenomeLandscape2019 -->
61
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
HIST1H1E.md
... ...
@@ -1,13 +1,17 @@
1 1
# HIST1H1E
2 2
## Overview
3 3
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.
4
+
5
+## History
6
+Mutations in this gene were first described in DLBCL in 2013 by Morin et al.<sup>3</sup> Mutations were subsequently reported in FL in 2017 by Krysiak et al<sup>4</sup> and in BL by Grande et al.<sup>5</sup>
7
+
4 8
## Relevance tier by entity
5 9
6 10
|Entity|Tier|Description |
7 11
|:------:|:----:|--------------------------------------|
8
-|BL |2 |relevance in BL not firmly established|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
12
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
13
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
14
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
11 15
12 16
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 17
... ...
@@ -31,10 +35,6 @@ This is one of several genes that encode linker histone proteins that are recurr
31 35
|FL |No |Yes |10.043 |0.000 |
32 36
33 37
34
-> [!NOTE]
35
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
36
-
37
-
38 38
## HIST1H1E Hotspots
39 39
40 40
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -65,6 +65,20 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
65 65
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HIST1H1E.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HIST1H1E_hg38.html)
66 66
67 67
![image](images/proteinpaint/HIST1H1E.svg)
68
+
68 69
## HIST1H1E Expression
69 70
![image](images/gene_expression/HIST1H1E_by_pathology.svg)
70
-<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
71
+
72
+## References
73
+1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
74
+2. *Li H, Kaminski MS, Li Y, Yildiz M, Ouillette P, Jones S, Fox H, Jacobi K, Saiya-Cork K, Bixby D, Lebovic D, Roulston D, Shedden K, Sabel M, Marentette L, Cimmino V, Chang AE, Malek SN. Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. Blood. 2014 Mar 6;123(10):1487-98. doi: 10.1182/blood-2013-05-500264. Epub 2014 Jan 16. PMID: 24435047; PMCID: PMC4729540.*
75
+3. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992*
76
+4. *Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390*
77
+
78
+5. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
79
+
80
+
81
+<!-- ORIGIN: 23699601 -->
82
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
83
+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
84
+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
HLA-DMB.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
41 41
## HLA-DMB Expression
42 42
![image](images/gene_expression/HLA-DMB_by_pathology.svg)
43 43
<!-- ORIGIN: Unknown -->
44
+<!-- BL: 2 -->
HLA-DQA1.md
... ...
@@ -1,7 +1,11 @@
1 1
# HLA-DQA1
2
-
2
+> [!NOTE]
3 3
Mutations in this gene are relatively rare in DLBCL overall. *Without further support, this gene may be migrated to Tier 2.*
4 4
5
+## History
6
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
7
+
8
+
5 9
## Relevance tier by entity
6 10
7 11
|Entity|Tier|Description |
... ...
@@ -26,12 +30,15 @@ Mutations in this gene are relatively rare in DLBCL overall. *Without further su
26 30
|FL |No |No |0 |0 |
27 31
28 32
29
-> [!NOTE]
30
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
31 33
32 34
## HLA-DQA1 Expression
33 35
![image](images/gene_expression/HLA-DQA1_by_pathology.svg)
34 36
37
+## References
38
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
39
+
40
+
35 41
<!-- FLAGGED FOR TIER 2 -->
36 42
<!-- ORPHANED -->
37 43
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
44
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
HLA-DQB1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
37 37
## HLA-DQB1 Expression
38 38
![image](images/gene_expression/HLA-DQB1_by_pathology.svg)
39 39
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40
+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
IKBKE.md
... ...
@@ -1,5 +1,8 @@
1 1
# IKBKE
2 2
3
+## History
4
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -24,9 +27,6 @@
24 27
|FL |No |No |0.000 |0 |
25 28
26 29
27
-> [!NOTE]
28
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
29
-
30 30
31 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKBKE_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKBKE_protein_hg38.html)
32 32
... ...
@@ -37,4 +37,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
![image](images/proteinpaint/IKBKE.svg)
38 38
## IKBKE Expression
39 39
![image](images/gene_expression/IKBKE_by_pathology.svg)
40
+
41
+
42
+## References
43
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
44
+
40 45
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
46
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
IRF1.md
... ...
@@ -1,5 +1,8 @@
1 1
# IRF1
2 2
3
+## History
4
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -29,9 +32,6 @@
29 32
|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
30 33
|chr5 |131823933 |131826458|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A131823933%2D131826458)|active_promoter |
31 34
32
-> [!NOTE]
33
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
34
-
35 35
36 36
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF1_protein_hg38.html)
37 37
... ...
@@ -42,4 +42,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
42 42
![image](images/proteinpaint/IRF1.svg)
43 43
## IRF1 Expression
44 44
![image](images/gene_expression/IRF1_by_pathology.svg)
45
+
46
+
47
+## References
48
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
49
+
45 50
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
51
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
LAPTM5.md
... ...
@@ -1,4 +1,6 @@
1 1
# LAPTM5
2
+## History
3
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
2 4
3 5
## Relevance tier by entity
4 6
... ...
@@ -31,9 +33,6 @@
31 33
|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
32 34
|chr1 |31229012 |31232011|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A31229012%2D31232011)|NA |
33 35
34
-> [!NOTE]
35
-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
36
-
37 36
38 37
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/LAPTM5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/LAPTM5_protein_hg38.html)
39 38
... ...
@@ -42,6 +41,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
42 41
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/LAPTM5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/LAPTM5_hg38.html)
43 42
44 43
![image](images/proteinpaint/LAPTM5.svg)
44
+
45 45
## LAPTM5 Expression
46 46
![image](images/gene_expression/LAPTM5_by_pathology.svg)
47
+
48
+## References
49
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
50
+
47 51
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
52
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
MGEA5.md
... ...
@@ -1,4 +1,6 @@
1 1
# MGEA5
2
+## History
3
+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
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3 5
## Relevance tier by entity
4 6
... ...
@@ -21,10 +23,6 @@
21 23
|FL |No |No |3.398 |0 |
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24
-> [!NOTE]
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-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
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-
27
-
28 26
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MGEA5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MGEA5_protein_hg38.html)
29 27
30 28
![image](images/proteinpaint/MGEA5_NM_012215.svg)
... ...
@@ -34,4 +32,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
34 32
![image](images/proteinpaint/MGEA5.svg)
35 33
## MGEA5 Expression
36 34
![image](images/gene_expression/MGEA5_by_pathology.svg)
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+
36
+
37
+## References
38
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
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+
37 40
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
41
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
N2RF2.md
... ...
@@ -1,5 +1,8 @@
1 1
# N2RF2
2 2
3
+## History
4
+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -15,15 +18,6 @@
15 18
|DLBCL |Reddy cohort |NA |
16 19
|DLBCL |Chapuy cohort |NA |
17 20
18
-## Mutation pattern and selective pressure estimates
19
-
20
-|
21
-
22
-
23
-> [!NOTE]
24
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
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-
26
-
27 21
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein_hg38.html)
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29 23
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_hg38.html)
... ...
@@ -31,4 +25,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
31 25
![image](images/proteinpaint/N2RF2.svg)
32 26
## N2RF2 Expression
33 27
![image](images/gene_expression/N2RF2_by_pathology.svg)
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+
29
+
30
+## References
31
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
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+
33
+
34 34
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
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+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
PDS5B.md
... ...
@@ -1,4 +1,6 @@
1 1
# PDS5B
2
+## History
3
+Mutations in this gene were first described in DLBCL in 2013 by Morin et al<sup>1</sup> and in FL in 2021 by Hübschmann et al.<sup>2</sup>
2 4
3 5
## Relevance tier by entity
4 6
... ...
@@ -25,11 +27,6 @@
25 27
|DLBCL |No |No |1.333 |6.726 |
26 28
|FL |No |No |0.000 |9.065 |
27 29
28
-
29
-> [!NOTE]
30
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
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-
32
-
33 30
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDS5B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDS5B_protein_hg38.html)
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35 32
![image](images/proteinpaint/PDS5B_NM_015032.svg)
... ...
@@ -39,4 +36,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 36
![image](images/proteinpaint/PDS5B.svg)
40 37
## PDS5B Expression
41 38
![image](images/gene_expression/PDS5B_by_pathology.svg)
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+
40
+## References
41
+1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992
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+
43
+2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
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+
42 45
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
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+<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
PRDM1.md
... ...
@@ -53,4 +53,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
53 53
![image](images/proteinpaint/PRDM1.svg)
54 54
## PRDM1 Expression
55 55
![image](images/gene_expression/PRDM1_by_pathology.svg)
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-<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
56
+<!-- ORIGIN: pasqualucciInactivationPRDM1BLIMP12006 -->
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+<!-- DLBCL: pasqualucciInactivationPRDM1BLIMP12006 -->
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+<!-- BL: 2 -->
PTEN.md
... ...
@@ -38,4 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 38
![image](images/proteinpaint/PTEN.svg)
39 39
## PTEN Expression
40 40
![image](images/gene_expression/PTEN_by_pathology.svg)
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-<!-- ORIGIN: NA -->
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+<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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+<!-- BL: loveGeneticLandscapeMutations2012 -->
TFAP4.md
... ...
@@ -1,10 +1,12 @@
1 1
# TFAP4
2
+## History
3
+Mutations in BL were first described by Grande et al.<sup>1</sup>
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3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------|
7
-|BL |1 |high-confidence BL gene|
9
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene|
8 10
9 11
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 12
... ...
@@ -23,10 +25,6 @@
23 25
|FL |No |No | 0.000 | 0.000 |
24 26
25 27
26
-> [!NOTE]
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-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
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-
29
-
30 28
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TFAP4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TFAP4_protein_hg38.html)
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32 30
![image](images/proteinpaint/TFAP4_NM_003223.svg)
... ...
@@ -41,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
41 39
## References
42 40
1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.*
43 41
<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
42
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->