HLA-B.md
... ...
@@ -1,7 +1,13 @@
1 1
# HLA-B
2 2
## Overview
3 3
Mutations in the HLA-B gene have been associated with a loss of cell surface expression of HLA class I molecules, which are essential for presenting tumor antigens to cytotoxic T cells. This is a common mechanism of immune escape in DLBCL. Deletions of this gene are more commonly reported than HLA-B mutations.<sup>1</sup> The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*. Different analytical strategies relating to the mapping of sequencing data and subtracting common germline variants can complicate the detection of mutations in this and other HLA genes. Likely owing to this, the rate of mutations is highly variable across studies and the true mutation rate has not been firmly established.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2019-12-10 : Wienand : PMBL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
HLA-C.md
... ...
@@ -1,7 +1,13 @@
1 1
# HLA-C
2 2
## Overview
3 3
Mutations in the HLA-C gene have been associated with a loss of cell surface expression of HLA class I molecules, which are essential for presenting tumor antigens to cytotoxic T cells. This is a common mechanism of immune escape in DLBCL. Deletions of this gene are more commonly reported than HLA-C mutations.<sup>1</sup> The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*. Different analytical strategies relating to the mapping of sequencing data and subtracting common germline variants can complicate the detection of mutations in this and other HLA genes. Likely owing to this, the rate of mutations is highly variable across studies and the true mutation rate has not been firmly established.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2023-11-15 : Gomez : PMBL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|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/HLA-C_by_pathology.svg)
40 46
<!-- ORIGIN: gomezUltraDeepSequencingReveals2023 -->
41 47
<!-- PMBL: gomezUltraDeepSequencingReveals2023 -->
48
+## References
49
+1. Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O’Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. Cancer Res Commun. 2023 Nov 15;3(11):2312–2330. PMCID: PMC10648575
HLA-DQA1.md
... ...
@@ -6,6 +6,12 @@ Mutations in this gene are relatively rare in DLBCL overall. *Without further su
6 6
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
7 7
8 8
9
+```mermaid
10
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
11
+timeline
12
+ title Publication timing
13
+ 2021-05-05 : Hübschmann : DLBCL
14
+```
9 15
## Relevance tier by entity
10 16
11 17
|Entity|Tier|Description |
HLA-DQB1.md
... ...
@@ -1,5 +1,11 @@
1 1
# HLA-DQB1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2022-07-06 : Burkhardt : 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/H
38 44
![image](images/gene_expression/HLA-DQB1_by_pathology.svg)
39 45
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40 46
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
47
+## References
48
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
HNF1B.md
... ...
@@ -1,5 +1,11 @@
1 1
# HNF1B
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2011-07-31 : Pasqualucci : 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/HNF1B_by_pathology.svg)
40 46
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
41 47
<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
48
+## References
49
+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
ICK.md
... ...
@@ -1,5 +1,11 @@
1 1
# ICK
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 |
... ...
@@ -36,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
36 42
![image](images/gene_expression/ICK_by_pathology.svg)
37 43
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
38 44
<!-- BL: loveGeneticLandscapeMutations2012 -->
45
+## References
46
+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
IER2.md
... ...
@@ -1,5 +1,11 @@
1 1
# IER2
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 |
... ...
@@ -30,3 +36,5 @@
30 36
![image](images/gene_expression/IER2_by_pathology.svg)
31 37
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
32 38
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
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
IFNGR1.md
... ...
@@ -1,5 +1,11 @@
1 1
# IFNGR1
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/I
39 45
![image](images/gene_expression/IFNGR1_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
IGLL5.md
... ...
@@ -1,5 +1,13 @@
1 1
# IGLL5
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-08-20 : Desch : PMBL
8
+ 2019-09-26 : Panea : BL
9
+ 2023-07-26 : Russler : FL
10
+```
3 11
## Relevance tier by entity
4 12
5 13
|Entity|Tier|Description |
... ...
@@ -53,3 +61,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
53 61
<!-- BL: paneaWholeGenomeLandscape2019 -->
54 62
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
55 63
<!-- BL: paneaWholeGenomeLandscape2019 -->
64
+## References
65
+1. 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
66
+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;
67
+3. 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.
IKBKB.md
... ...
@@ -1,5 +1,13 @@
1 1
# IKBKB
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2011-11-03 : Rossi : MZL
8
+ 2017-10-10 : Reddy : DLBCL
9
+ 2019-12-10 : Wienand : PMBL
10
+```
3 11
## Relevance tier by entity
4 12
5 13
|Entity|Tier|Description |
... ...
@@ -43,3 +51,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
43 51
<!-- MZL: rossiAlterationBIRC3Multiple2011a -->
44 52
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
45 53
<!-- PMBL: wienandGenomicAnalysesFlowsorted2019b -->
54
+## References
55
+1. Rossi D, Deaglio S, Dominguez-Sola D, Rasi S, Vaisitti T, Agostinelli C, Spina V, Bruscaggin A, Monti S, Cerri M, Cresta S, Fangazio M, Arcaini L, Lucioni M, Marasca R, Thieblemont C, Capello D, Facchetti F, Kwee I, Pileri SA, Foà R, Bertoni F, Dalla-Favera R, Pasqualucci L, Gaidano G. Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma. Blood. 2011 Nov 3;118(18):4930–4934. PMID: 21881048
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;171(2):481-494.e15.
57
+3. Wienand K, Chapuy B, Stewart C, Dunford AJ, Wu D, Kim J, Kamburov A, Wood TR, Cader FZ, Ducar MD, Thorner AR, Nag A, Heubeck AT, Buonopane MJ, Redd RA, Bojarczuk K, Lawton LN, Armand P, Rodig SJ, Fromm JR, Getz G, Shipp MA. Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion. Blood Adv. 2019 Dec 10;3(23):4065–4080. PMCID: PMC6963251
IKZF3.md
... ...
@@ -1,7 +1,14 @@
1 1
# IKZF3
2 2
## Overview
3 3
IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription factor involved in regulating B-cell development and function. Mutations in IKZF3 can lead to transcriptional dysregulation and contribute to the pathogenesis of B-cell neoplasms. IKZF3 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. IKZF3 has multiple hot spot mutations in DLBCL. The most common, L162R, has been identified as a driver in CLL. In that context, it alters DNA binding specificity and causes hyperactivation of B-cell receptor (BCR) signaling and overexpression of NF-κB target genes.<sup>1</sup> While primarily studied in CLL, the functional effects of IKZF3 mutations could have implications for other B-cell malignancies, including 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
+ 2019-09-26 : Panea : BL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
IL16.md
... ...
@@ -1,6 +1,7 @@
1 1
# IL16
2 2
## Overview
3 3
The IL16 gene, which encodes a pro-inflammatory cytokine, plays a role in immune responses. IL-16 is highly expressed in the activated B-cell-like (ABC) subtype of DLBCL compared to the germinal center B-cell-like (GCB) subtype. The role of mutations in lymphomagenesis is not understood. Overall, the mutation rate of IL16 is relatively low in DLBCL. *Without further support, this gene may be migrated to Tier 2.*
4
+## History
4 5
5 6
## Relevance tier by entity
6 7
IL6.md
... ...
@@ -1,5 +1,12 @@
1 1
# IL6
2 2
3
+## History
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2018-05-01 : Chapuy : DLBCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
39 46
![image](images/gene_expression/IL6_by_pathology.svg)
40 47
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 48
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
49
+## References
50
+1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
INO80.md
... ...
@@ -1,5 +1,11 @@
1 1
# INO80
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-01-01 : Zhang : 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/I
39 45
![image](images/gene_expression/INO80_by_pathology.svg)
40 46
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41 47
<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
48
+## References
49
+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;
IRF1.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 |
LAPTM5.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 |
LCOR.md
... ...
@@ -1,7 +1,13 @@
1 1
# LCOR
2 2
## Overview
3 3
LCOR (Ligand Dependent Nuclear Receptor Corepressor) is involved in the regulation of gene expression by acting as a corepressor for various nuclear receptors and transcription factors. It influences chromatin structure and gene transcription, which can impact cell growth and differentiation. Although recurrently mutated in DLBCL, owing to different annotations of this gene and C10orf12 in hg19 and hg38, there is some confusion about the mutation rate.
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 |
... ...
@@ -44,3 +50,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
44 50
<!-- ORIGIN: 30275490 -->
45 51
<!-- BL: 2 -->
46 52
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
53
+## References
54
+1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379
LIN54.md
... ...
@@ -1,5 +1,11 @@
1 1
# LIN54
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/L
39 45
![image](images/gene_expression/LIN54_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.
LRP12.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL 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 : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
LRRN3.md
... ...
@@ -1,5 +1,12 @@
1 1
# LRRN3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+ 2021-04-01 : Sarkozy : 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/L
41 48
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
42 49
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
43 50
<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
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. Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765–1776. PMID: 32961552
LYN.md
... ...
@@ -1,7 +1,13 @@
1 1
# LYN
2 2
## Overview
3 3
LYN mutations have been reported in DLBCL but the rate is relatively rare in most cohorts. The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. *Without further support, this gene may be migrated to Tier 2.*
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2018-05-01 : Chapuy : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
... ...
@@ -40,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
40 46
<!-- FLAGGED FOR TIER 2 -->
41 47
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
42 48
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
49
+## References
50
+1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
MAGEC1.md
... ...
@@ -1,5 +1,11 @@
1 1
# MAGEC1
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 |
... ...
@@ -45,3 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
45 51
![image](images/gene_expression/MAGEC1_by_pathology.svg)
46 52
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
47 53
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
54
+## References
55
+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.
MAGT1.md
... ...
@@ -1,5 +1,11 @@
1 1
# MAGT1
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/MAGT1_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.
MALAT1.md
... ...
@@ -1,5 +1,11 @@
1 1
# MALAT1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2018-10-01 : Arthur : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -37,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 43
![image](images/gene_expression/MALAT1_by_pathology.svg)
38 44
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
39 45
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
46
+## References
47
+1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379
MAP3K6.md
... ...
@@ -1,5 +1,11 @@
1 1
# MAP3K6
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/M
38 44
![image](images/gene_expression/MAP3K6_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