MYC.md
... ...
@@ -2,6 +2,16 @@
2 2
## Overview
3 3
MYC 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
5
+## History
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 1992-12-01 : Johnston : BL
11
+ 2001-07-19 : Pasqualucci : DLBCL
12
+ 2017-07-27 : Jallades : MZL
13
+ 2021-07-15 : Duns : PMBL
14
+```
5 15
## Relevance tier by entity
6 16
7 17
|Entity|Tier|Description |
NOL9.md
... ...
@@ -1,9 +1,17 @@
1 1
# NOL9
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2016-09-08 : Spina : MZL
8
+ 2018-04-12 : Schmitz : DLBCL
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
9 17
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -45,3 +53,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
45 53
<!-- ORIGIN: spinaGeneticsNodalMarginal2016b -->
46 54
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
47 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.
58
+2. 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
P2RY2.md
... ...
@@ -1,5 +1,11 @@
1 1
# P2RY2
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/P
38 44
![image](images/gene_expression/P2RY2_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
P2RY8.md
... ...
@@ -1,6 +1,14 @@
1 1
# P2RY8
2 2
P2RY8 encodes a G protein–coupled receptor that is expressed on germinal center B cells. Signals through this receptor promote confinement of B cells to the GC niche.<sup>1</sup> Downstream signaling through Galpha13 (encoded by GNA13) and S1PR2 is distrupted by mutations of one of these genes in GC lymphomas including the GCB subgroup of DLBCL<sup>2</sup> and BL.<sup>1</sup>
3 3
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2012-03-06 : Lohr : DLBCL
10
+ 2014-12-11 : Muppidi : BL
11
+```
4 12
## Relevance tier by entity
5 13
6 14
|Entity|Tier|Description |
PABPC4L.md
... ...
@@ -1,5 +1,11 @@
1 1
# PABPC4L
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : 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/P
38 44
![image](images/gene_expression/PABPC4L_by_pathology.svg)
39 45
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40 46
<!-- BL: paneaWholeGenomeLandscape2019 -->
47
+## References
48
+1. 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;
PCBP1.md
... ...
@@ -1,5 +1,11 @@
1 1
# PCBP1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-10-04 : Schmitz : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -53,3 +59,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
53 59
![image](images/gene_expression/PCBP1_by_pathology.svg)
54 60
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
55 61
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
62
+## References
63
+1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867
RUNX1.md
... ...
@@ -1,5 +1,11 @@
1 1
# RUNX1
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/R
39 45
![image](images/gene_expression/RUNX1_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.
S1PR1.md
... ...
@@ -1,5 +1,12 @@
1 1
# S1PR1
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2020-07-30 : Pararajalingam : MCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
36 43
![image](images/gene_expression/S1PR1_by_pathology.svg)
37 44
<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
38 45
<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
46
+## References
47
+1. Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572–584. PMCID: PMC7440974