GGTLA4.md
... ...
@@ -1,5 +1,12 @@
1 1
# GGTLA4
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2012-12-01 : Love : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -32,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
32 39
![image](images/gene_expression/GGTLA4_by_pathology.svg)
33 40
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34 41
<!-- BL: loveGeneticLandscapeMutations2012 -->
42
+## References
43
+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
GOLGA5.md
... ...
@@ -1,5 +1,11 @@
1 1
# GOLGA5
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-10-10 : Reddy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -39,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
39 45
![image](images/gene_expression/GOLGA5_by_pathology.svg)
40 46
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41 47
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
48
+## References
49
+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.
GRB2.md
... ...
@@ -1,7 +1,14 @@
1 1
# GRB2
2 2
## Overview
3 3
GRB2 (Growth factor receptor-bound protein 2) is an adaptor protein that links receptor tyrosine kinases to the Ras signaling pathway through its SH2 and SH3 domains. The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*. While direct evidence of GRB2 mutations in DLBCL is limited, its established role in other cancers and signal transduction pathways suggests that it may contribute to lymphomagenesis. Further research is needed to elucidate its specific role in DLBCL.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-31 : Pasqualucci : DLBCL
10
+ 2019-09-26 : Panea : BL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
... ...
@@ -46,3 +53,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
46 53
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
47 54
<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
48 55
<!-- BL: paneaWholeGenomeLandscape2019 -->
56
+## References
57
+1. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011 Jul 31;43(9):830–837. PMCID: PMC3297422
58
+2. 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;
GRHPR.md
... ...
@@ -2,7 +2,13 @@
2 2
## Overview
3 3
GRHPR 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. The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*. Coding and non-coding mutations in GRHPR are a feature of the MCD genetic subgroup of DLBCL.<sup>1</sup> Further research is needed to elucidate the specific role of GRHPR mutations in DLBCL.
4 4
5
-
5
+## History
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2018-10-01 : Arthur : DLBCL
11
+```
6 12
## Relevance tier by entity
7 13
8 14
|Entity|Tier|Description |
GRIK5.md
... ...
@@ -1,5 +1,11 @@
1 1
# GRIK5
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
38 44
![image](images/gene_expression/GRIK5_by_pathology.svg)
39 45
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 46
<!-- BL: loveGeneticLandscapeMutations2012 -->
47
+## References
48
+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
GRIN2A.md
... ...
@@ -1,5 +1,11 @@
1 1
# GRIN2A
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -36,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
36 42
![image](images/gene_expression/GRIN2A_by_pathology.svg)
37 43
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 44
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
45
+## References
46
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
GSG2.md
... ...
@@ -1,5 +1,11 @@
1 1
# GSG2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2018-04-12 : Schmitz : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -39,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
39 45
![image](images/gene_expression/GSG2_by_pathology.svg)
40 46
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
41 47
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
48
+## References
49
+1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183
HDAC7.md
... ...
@@ -1,5 +1,11 @@
1 1
# HDAC7
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -39,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
39 45
![image](images/gene_expression/HDAC7_by_pathology.svg)
40 46
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 47
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
48
+## References
49
+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
HEPH.md
... ...
@@ -1,5 +1,11 @@
1 1
# HEPH
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -36,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
36 42
![image](images/gene_expression/HEPH_by_pathology.svg)
37 43
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 44
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
45
+## References
46
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
IKBKE.md
... ...
@@ -3,6 +3,12 @@
3 3
## History
4 4
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
5 5
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2021-05-05 : H : DLBCL
11
+```
6 12
## Relevance tier by entity
7 13
8 14
|Entity|Tier|Description |
IL4R.md
... ...
@@ -1,7 +1,14 @@
1 1
# IL4R
2 2
## Overview
3 3
Mutations in IL4R have been identified in various types of B-cell lymphomas, particularly primary mediastinal large B-cell lymphoma (PMBCL) and DLBCL. IL4R 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. IL4R mutations are found in approximately 24.2% of primary PMBCL cases. These mutations are commonly single nucleotide variants in exon 8, resulting in the I242N amino acid change. This leads to constitutive activation of the JAK-STAT signaling pathway and upregulation of downstream cytokine expression profiles and B cell-specific antigens.<sup>1,2</sup> In DLBCL, IL4R mutations are more rare and tend to occur within the GCB subgroup.<sup>2</sup>
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2018-05-03 : Vigan : PMBL
10
+ 2021-07-15 : Duns : DLBCL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
MAP2K1.md
... ...
@@ -1,5 +1,12 @@
1 1
# MAP2K1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2015-03-01 : Shin : DLBCL
8
+ 2016-08-25 : Louissaint : FL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -48,3 +55,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
48 55
<!-- ORIGIN: shinBRAFV600EMAP2K12015 -->
49 56
<!-- DLBCL: shinBRAFV600EMAP2K12015 -->
50 57
<!-- FL: louissaintPediatrictypeNodalFollicular2016a -->
58
+## References
59
+1. Shin SY, Lee ST, Kim HJ, Ki CS, Jung CW, Kim JW, Kim SH. BRAF V600E and MAP2K1 mutations in hairy cell leukemia and splenic marginal zone lymphoma cases. Ann Lab Med. 2015 Mar;35(2):257–259. PMCID: PMC4330180
60
+2. Louissaint A, Schafernak KT, Geyer JT, Kovach AE, Ghandi M, Gratzinger D, Roth CG, Paxton CN, Kim S, Namgyal C, Morin R, Morgan EA, Neuberg DS, South ST, Harris MH, Hasserjian RP, Hochberg EP, Garraway LA, Harris NL, Weinstock DM. Pediatric-type nodal follicular lymphoma: a biologically distinct lymphoma with frequent MAPK pathway mutations. Blood. 2016 Aug 25;128(8):1093–1100. PMCID: PMC5000844
MEF2C.md
... ...
@@ -1,7 +1,13 @@
1 1
# MEF2C
2 2
## Overview
3 3
MEF2C 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.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2018-10-01 : Arthur : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
PCLO.md
... ...
@@ -1,6 +1,11 @@
1 1
# PCLO
2
-## Overview
3
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-03-06 : Lohr : DLBCL
8
+```
4 9
## Relevance tier by entity
5 10
6 11
|Entity|Tier|Description |
POU2AF1.md
... ...
@@ -1,11 +1,18 @@
1 1
# POU2AF1
2 2
## Overview
3 3
POU2AF1 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.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-01-26 : Krysiak : FL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
8 14
|:------:|:----:|--------------------------|
15
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
9 16
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated|
10 17
|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated |
11 18
... ...
@@ -56,3 +63,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
56 63
![image](images/gene_expression/POU2AF1_by_pathology.svg)
57 64
<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
58 65
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
66
+## References
67
+1. 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
POU2F2.md
... ...
@@ -1,5 +1,12 @@
1 1
# POU2F2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-01-01 : Zhang : DLBCL
8
+ 2017-01-26 : Krysiak : FL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -49,3 +56,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
49 56
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
50 57
<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
51 58
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
59
+## References
60
+1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan;
61
+2. 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
PTPRD.md
... ...
@@ -1,5 +1,11 @@
1 1
# PTPRD
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2016-09-08 : Spina : MZL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -47,3 +53,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 53
![image](images/gene_expression/PTPRD_by_pathology.svg)
48 54
<!-- ORIGIN: spinaGeneticsNodalMarginal2016b -->
49 55
<!-- MZL: spinaGeneticsNodalMarginal2016b -->
56
+## References
57
+1. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373.
RRAGC.md
... ...
@@ -1,5 +1,11 @@
1 1
# RRAGC
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2016-02-02 : Okosun : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -41,3 +47,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
41 47
![image](images/gene_expression/RRAGC_by_pathology.svg)
42 48
<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
43 49
<!-- DLBCL: okosunRecurrentMTORC1activatingRRAGC2016a -->
50
+## References
51
+1. Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016 Feb;48(2):183–188. PMCID: PMC4731318
S1PR2.md
... ...
@@ -1,7 +1,14 @@
1 1
# S1PR2
2 2
## Overview
3 3
S1PR2 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.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-27 : Morin : DLBCL
10
+ 2014-12-11 : Muppidi : BL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
... ...
@@ -38,9 +45,6 @@ S1PR2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
38 45
|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
39 46
|chr19 |10340142 |10341764|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A10340142%2D10341764)|active_promoter |
40 47
41
-> [!NOTE]
42
-> First described in BL in 2014 by [Muppidi JR](https://pubmed.ncbi.nlm.nih.gov/25274307)
43
-
44 48
45 49
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S1PR2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/S1PR2_protein_hg38.html)
46 50
... ...
@@ -54,3 +58,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
54 58
<!-- ORIGIN: 21796119 -->
55 59
<!-- BL: muppidiLossSignalingGa132014b -->
56 60
<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
61
+## References
62
+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 SJM, 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. PMCID: PMC3210554
63
+2. Muppidi J, Schmitz R, Green JA, Green JA, Xiao W, Larsen AB, Braun S, An J, Xu Y, Rosenwald A, Ott G, Gascoyne R, Rimsza L, Campo E, Jaffe E, Delabie J, Smeland E, Braziel R, Tubbs R, Cook J, Weisenburger D, Chan W, Vaidehi N, Staudt L, Cyster J. Loss of signaling via Gα13 in germinal center B cell-derived lymphoma. Nature. 2014;516:254–258.
TNFAIP3.md
... ...
@@ -1,5 +1,13 @@
1 1
# TNFAIP3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2009-05-11 : Schmitz : PMBL
8
+ 2009-06-04 : Compagno : DLBCL
9
+ 2011-11-03 : Rossi : MZL
10
+```
3 11
## Relevance tier by entity
4 12
5 13
|Entity|Tier|Description |
TNFRSF14.md
... ...
@@ -1,9 +1,17 @@
1 1
# TNFRSF14
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2010-11-15 : Cheung : FL
8
+ 2016-09-08 : Spina : MZL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
6 13
|:------:|:----:|--------------------------------------|
14
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
7 15
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
8 16
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
9 17
VMA21.md
... ...
@@ -1,5 +1,11 @@
1 1
# VMA21
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2021-05-05 : H : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -36,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/V
36 42
![image](images/gene_expression/VMA21_by_pathology.svg)
37 43
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
38 44
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
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