ATP6V1A.md
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View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATP6V1A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATP6V1A_protein_hg38.html)
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-![image](images/proteinpaint/ATP6V1A_NM_001690.svg)
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+![](images/proteinpaint/ATP6V1A_NM_001690.svg)
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View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATP6V1A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATP6V1A_hg38.html)
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-![image](images/proteinpaint/ATP6V1A.svg)
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## ATP6V1A Expression
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-![image](images/gene_expression/ATP6V1A_by_pathology.svg)
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## References
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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
ATR.md
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# ATR
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## History
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Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
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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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View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATR_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATR_protein_hg38.html)
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-![image](images/proteinpaint/ATR_NM_001184.svg)
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+![](images/proteinpaint/ATR_NM_001184.svg)
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View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATR.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATR_hg38.html)
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-![image](images/proteinpaint/ATR.svg)
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## ATR Expression
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-![image](images/gene_expression/ATR_by_pathology.svg)
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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.*
B2M.md
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# B2M
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## Overview
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2015-02-12 : Reichel : PMBL
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2020-07-30 : Pararajalingam : MCL
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```
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## Relevance tier by entity
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|Entity|Tier|Description |
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|FL |No |Yes |54.190 |326.834 |
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-> [!NOTE]
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-> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
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## B2M Hotspots
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View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B2M_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/B2M_protein_hg38.html)
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-![image](images/proteinpaint/B2M_NM_004048.svg)
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+![](images/proteinpaint/B2M_NM_004048.svg)
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View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B2M.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/B2M_hg38.html)
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-![image](images/proteinpaint/B2M.svg)
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## B2M Expression
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-![image](images/gene_expression/B2M_by_pathology.svg)
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<!-- FL: morinFrequentMutationHistonemodifying2011 -->
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<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
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<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
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## References
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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
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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