BTG1.md
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## Overview
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BTG1 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. These mutations are a feature of the MCD genetic subgroup of DLBCL.<sup>1</sup> Mutations in the BTG1 gene have been implicated in the pathogenesis and progression of diffuse large B-cell lymphoma (DLBCL) through functional exploration in vivo. Knock-out of BTG1 did not lead to spontaneous lymphomagenesis but enhanced the lymphoproliferation induced by VavP-BCL2 and promoted lymphoma dissemination in xenotransplantation experiments.<sup>2</sup> Another study demonstrated that specific BTG1 mutations afford germinal center (GC) B cells with a fitness advantage relative to un-mutated counterparts.<sup>3</sup>
4 4
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2011-07-27 : Morin : DLBCL
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+ 2021-04-01 : Sarkozy : PMBL
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+ 2022-07-06 : Burkhardt : BL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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@@ -82,12 +90,18 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
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## BTG1 Expression
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![image](images/gene_expression/BTG1_by_pathology.svg)
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+
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+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
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+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
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+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
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+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
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## References
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+
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1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*
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2. *Delage L, Lambert M, Bardel É, Kundlacz C, Chartoire D, Conchon A, Peugnet AL, Gorka L, Auberger P, Jacquel A, Soussain C, Destaing O, Delecluse HJ, Delecluse S, Merabet S, Traverse-Glehen A, Salles G, Bachy E, Billaud M, Ghesquières H, Genestier L, Rouault JP, Sujobert P. BTG1 inactivation drives lymphomagenesis and promotes lymphoma dissemination through activation of BCAR1. Blood. 2023 Mar 9;141(10):1209-1220. doi: 10.1182/blood.2022016943. PMID: 36375119.*
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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.*
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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.*
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-<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
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-<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
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-<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
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-<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
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+
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+5. 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
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+6. 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
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+
DNAH5.md
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@@ -1,9 +1,17 @@
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# DNAH5
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-
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+## History
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2013-08-15 : Morin : DLBCL
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+ 2017-07-27 : Jallades : MZL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
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|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
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<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
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<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
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+## References
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+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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+2. Jallades L, Baseggio L, Sujobert P, Huet S, Chabane K, Callet-Bauchu E, Verney A, Hayette S, Desvignes JP, Salgado D, Levy N, Béroud C, Felman P, Berger F, Magaud JP, Genestier L, Salles G, Traverse-Glehen A. Exome sequencing identifies recurrent BCOR alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma. Haematologica. 2017 Oct;102(10):1758–1766. PMCID: PMC5622860
DNMT1.md
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# DNMT1
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-
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+## History
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+
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2019-09-26 : Panea : BL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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![image](images/gene_expression/DNMT1_by_pathology.svg)
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<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
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<!-- BL: paneaWholeGenomeLandscape2019 -->
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+## References
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+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;
DNMT3A.md
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# DNMT3A
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-
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+## History
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+
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2017-10-10 : Reddy : DLBCL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
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![image](images/gene_expression/DNMT3A_by_pathology.svg)
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<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
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<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
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+## References
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+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.
DOCK1.md
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# DOCK1
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-
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+## History
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+
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2018-05-01 : Chapuy : DLBCL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
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![image](images/gene_expression/DOCK1_by_pathology.svg)
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<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
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<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
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+## References
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+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
DSG4.md
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@@ -1,5 +1,12 @@
1 1
# DSG4
2
-
2
+## History
3
+
4
+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2013-08-15 : Morin : DLBCL
9
+```
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## 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/D
39 46
![image](images/gene_expression/DSG4_by_pathology.svg)
40 47
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 48
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
49
+## References
50
+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