MAP4K4.md
... ...
@@ -1,5 +1,11 @@
1 1
# MAP4K4
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/M
39 45
![image](images/gene_expression/MAP4K4_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.
MAP7D1.md
... ...
@@ -1,5 +1,11 @@
1 1
# MAP7D1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2023-07-26 : Russler : 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/M
36 42
![image](images/gene_expression/MAP7D1_by_pathology.svg)
37 43
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38 44
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
45
+## References
46
+1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.
MARK1.md
... ...
@@ -1,5 +1,11 @@
1 1
# MARK1
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/M
39 45
![image](images/gene_expression/MARK1_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.
MCL1.md
... ...
@@ -1,7 +1,15 @@
1 1
# MCL1
2 2
## Overview
3 3
MCL1 (Myeloid Cell Leukemia 1) is a member of the BCL2 family of proteins that play a critical role in inhibiting apoptosis. It is frequently overexpressed and sometimes mutated in DLBCL.<sup>1,2</sup> Recurrent chromosomal gains and amplifications of the MCL1 locus occur are frequent in ABC-DLBCLs.<sup>1</sup> MCL1 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
+ 2017-10-10 : Reddy : DLBCL
10
+ 2019-09-26 : Panea : BL
11
+ 2021-07-15 : Duns : PMBL
12
+```
5 13
## Relevance tier by entity
6 14
7 15
|Entity|Tier|Description |
... ...
@@ -36,9 +44,6 @@ MCL1 (Myeloid Cell Leukemia 1) is a member of the BCL2 family of proteins that p
36 44
|:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------:|:------------------:|
37 45
|chr1 |150550814 |150552135|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A150550814%2D150552135)|NA |
38 46
39
-> [!NOTE]
40
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
41
-
42 47
43 48
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MCL1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MCL1_protein_hg38.html)
44 49
... ...
@@ -51,10 +56,13 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
51 56
## MCL1 Expression
52 57
![image](images/gene_expression/MCL1_by_pathology.svg)
53 58
54
-## References
55
-1. *Wenzel, S., Grau, M., Mavis, C., Hailfinger, S., Wolf, A., Madle, H., Deeb, G., Dörken, B., Thome, M., Lenz, P., Dirnhofer, S., Hernandez-Ilizaliturri, F., Tzankov, A., & Lenz, G. (2013). MCL1 is deregulated in subgroups of diffuse large B-cell lymphoma. Leukemia, 27, 1381-1390. https://doi.org/10.1038/leu.2012.367.*
56
-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 5;171(2):481-494.e15. doi: 10.1016/j.cell.2017.09.027. PMID: 28985567; PMCID: PMC5659841.*
59
+
57 60
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
58 61
<!-- BL: paneaWholeGenomeLandscape2019 -->
59 62
<!-- BL: paneaWholeGenomeLandscape2019 -->
60 63
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
64
+## References
65
+1. *Wenzel, S., Grau, M., Mavis, C., Hailfinger, S., Wolf, A., Madle, H., Deeb, G., Dörken, B., Thome, M., Lenz, P., Dirnhofer, S., Hernandez-Ilizaliturri, F., Tzankov, A., & Lenz, G. (2013). MCL1 is deregulated in subgroups of diffuse large B-cell lymphoma. Leukemia, 27, 1381-1390. https://doi.org/10.1038/leu.2012.367.*
66
+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 5;171(2):481-494.e15. doi: 10.1016/j.cell.2017.09.027. PMID: 28985567; PMCID: PMC5659841.*
67
+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;*
68
+4. *Duns G, Viganò E, Ennishi D, Sarkozy C, Hung SS, Chavez E, Takata K, Rushton C, Jiang A, Ben-Neriah S, Woolcock BW, Slack GW, Hsi ED, Craig JW, Hilton LK, Shah SP, Farinha P, Mottok A, Gascoyne RD, Morin RD, Savage KJ, Scott DW, Steidl C. Characterization of DLBCL with a PMBL gene expression signature. Blood. 2021 Jul 15;138(2):136–148. PMID: 33684939*
MECOM.md
... ...
@@ -1,5 +1,11 @@
1 1
# MECOM
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/M
39 45
![image](images/gene_expression/MECOM_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.
MET.md
... ...
@@ -1,5 +1,11 @@
1 1
# MET
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/M
39 45
![image](images/gene_expression/MET_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.
MGA.md
... ...
@@ -1,11 +1,19 @@
1 1
# MGA
2 2
## Overview
3 3
MGA acts as a transcriptional repressor and interacts with MYC, a well-known oncogene. Mutations in MGA have been described in DLBCL.<sup>1</sup> One study suggested MGA mutations were more common in DLBCLs in patients of African ancestry.<sup>2</sup> The mutation pattern in MGA is consistent with a role as a tumour suppressor gene.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2013-01-01 : Zhang : DLBCL
10
+ 2017-07-27 : Jallades : MZL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
8 15
|:------:|:----:|--------------------------|
16
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
9 17
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 18
11 19
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MGEA5.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2021-05-05 : H : FL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
MIR142.md
... ...
@@ -1,5 +1,12 @@
1 1
# MIR142
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-10-1 : Kwanhian : DLBCL
8
+ 2019-03-21 : Grande : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -31,3 +38,6 @@
31 38
<!-- ORIGIN: kwanhianMicroRNA142Mutated202012b -->
32 39
<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
33 40
<!-- DLBCL: kwanhianMicroRNA142Mutated202012b -->
41
+## References
42
+1. Kwanhian W, Lenze D, Alles J, Motsch N, Barth S, Döll C, Imig J, Hummel M, Tinguely M, Trivedi P, Lulitanond V, Meister G, Renner C, Grässer FA. MicroRNA-142 is mutated in about 20% of diffuse large B-cell lymphoma. Cancer Med. 2012 Oct;1(2):141–155. PMCID: PMC3544448
43
+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.
MKI67.md
... ...
@@ -1,5 +1,12 @@
1 1
# MKI67
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-10-04 : Schmitz : BL
8
+ 2023-07-26 : Russler : FL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -41,3 +48,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
41 48
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
42 49
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
43 50
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
51
+## References
52
+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
53
+2. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.
MME.md
... ...
@@ -1,5 +1,11 @@
1 1
# MME
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/M
38 44
![image](images/gene_expression/MME_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;
MPDZ.md
... ...
@@ -1,5 +1,12 @@
1 1
# MPDZ
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+ 2015-02-12 : Reichel : PMBL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -41,3 +48,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
41 48
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
42 49
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
43 50
<!-- PMBL: reichelFlowSortingExome2015a -->
51
+## References
52
+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
53
+2. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972
MPEG1.md
... ...
@@ -1,11 +1,18 @@
1 1
# MPEG1
2 2
## Overview
3 3
Mutations in MPEG1 have been described in DLBCL<sup>1</sup> with the overall rate of mutations somewhat variable across studies. MPEG1 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. Coding and non-coding MPEG1 mutations are a feature of the MCD genetic subgroup of DLBCL.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2013-08-15 : Morin : DLBCL
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|
10 17
11 18
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MRGPRF.md
... ...
@@ -1,5 +1,11 @@
1 1
# MRGPRF
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/M
36 42
![image](images/gene_expression/MRGPRF_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.
MS4A1.md
... ...
@@ -1,7 +1,14 @@
1 1
# MS4A1
2 2
## Overview
3 3
MS4A1 encodes the CD20 protein, which is the target of rituximab and other therapeutic monoclonal antibodies. MS4A1 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. In relapsed DLBCLs, MS4A1 is sometimes mutated and these mutations have been shown to reduce CD20 expression.<sup>1</sup>
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2019-09-05 : Mottok : PMBL
10
+ 2020-07-14 : Rushton : DLBCL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
MSH2.md
... ...
@@ -1,5 +1,11 @@
1 1
# MSH2
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/M
39 45
![image](images/gene_expression/MSH2_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.
MSH6.md
... ...
@@ -1,5 +1,11 @@
1 1
# MSH6
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/M
39 45
![image](images/gene_expression/MSH6_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.
MTOR.md
... ...
@@ -1,7 +1,14 @@
1 1
# MTOR
2 2
## Overview
3 3
Although mutations in MTOR have been reported in DLBCL<sup>1</sup> and some BL, their role in lymphomagenesis has not been thoroughly studied.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2013-01-01 : Zhang : DLBCL
10
+ 2019-09-26 : Panea : BL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
MYB.md
... ...
@@ -1,5 +1,12 @@
1 1
# MYB
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-10-10 : Reddy : DLBCL
8
+ 2019-08-20 : Desch : PMBL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -41,3 +48,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
41 48
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
42 49
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
43 50
<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
51
+## References
52
+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.
53
+2. Desch AK, Hartung K, Botzen A, Brobeil A, Rummel M, Kurch L, Georgi T, Jox T, Bielack S, Burdach S, Classen CF, Claviez A, Debatin KM, Ebinger M, Eggert A, Faber J, Flotho C, Frühwald M, Graf N, Jorch N, Kontny U, Kramm C, Kulozik A, Kühr J, Sykora KW, Metzler M, Müller HL, Nathrath M, Nüßlein T, Paulussen M, Pekrun A, Reinhardt D, Reinhard H, Rössig C, Sauerbrey A, Schlegel PG, Schneider DT, Scheurlen W, Schweigerer L, Simon T, Suttorp M, Vorwerk P, Schmitz R, Kluge R, Mauz-Körholz C, Körholz D, Gattenlöhner S, Bräuninger A. Genotyping circulating tumor DNA of pediatric Hodgkin lymphoma. Leukemia. 2020 Jan;34(1):151–166. PMID: 31431735
MYBPC2.md
... ...
@@ -1,5 +1,11 @@
1 1
# MYBPC2
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/M
39 45
![image](images/gene_expression/MYBPC2_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
MYCBP2.md
... ...
@@ -3,6 +3,12 @@
3 3
## History
4 4
Mutations in this gene were first described in 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 : FL
11
+```
6 12
## Relevance tier by entity
7 13
8 14
|Entity|Tier|Description |