ATP11C.md
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# ATP11C
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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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+ 2014-05-08 : Zhang : MCL
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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/ATP11C_by_pathology.svg)
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<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
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<!-- MCL: zhangGenomicLandscapeMantle2014 -->
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+## References
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+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.
BCR.md
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## BCR Expression
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![image](images/gene_expression/BCR_by_pathology.svg)
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<!-- ORIGIN: Unknown -->
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+## References
BIRC3.md
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# BIRC3
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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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+ 2011-11-03 : Rossi : MZL
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+ 2013-11-05 : Be : MCL
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+ 2018-10-01 : Arthur : DLBCL
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+ 2021-07-15 : Duns : PMBL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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<!-- MZL: rossiAlterationBIRC3Multiple2011a -->
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<!-- MCL: beaLandscapeSomaticMutations2013 -->
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<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
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+## References
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+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
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+2. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436
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+3. 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
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+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
BLK.md
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## BLK Expression
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![image](images/gene_expression/BLK_by_pathology.svg)
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<!-- ORIGIN: Unknown -->
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+## References
BRAF.md
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## Overview
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BRAF mutations, particularly the BRAF V600E hot spot mutation, are primarily associated with hairy cell leukemia and are rare in other B-cell lymphomas. These mutations play a crucial role in the pathogenesis of HCL and have important diagnostic and therapeutic implications. Although they are rare, mutations in BRAF are reproducibly observed in some DLBCLs. Another hot spot, D594A, occurs in DLBCL. The role of these in lymphomagenesis remains poorly understood but functional evidence suggests they may contribute to aneuploidy.<sup>1<sup>
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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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+ 2011-06-16 : Tiacci : DLBCL
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+ 2012-12-01 : Love : BL
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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_tier1.png)|1|high-confidence MZL gene|
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|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
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|![BL](images/icons/Tier2_BL.png) |2 |relevance in BL not firmly established|
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BRD4.md
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# BRD4
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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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+ 2012-12-01 : Love : 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/BRD4_by_pathology.svg)
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<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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<!-- BL: loveGeneticLandscapeMutations2012 -->
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+## References
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+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
C6orf27.md
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# C6orf27
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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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+ 2012-12-01 : Love : 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/C6orf27_by_pathology.svg)
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<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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<!-- BL: loveGeneticLandscapeMutations2012 -->
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+## References
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+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
CAD.md
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# CAD
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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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+ 2012-12-01 : Love : 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/CAD_by_pathology.svg)
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<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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<!-- BL: loveGeneticLandscapeMutations2012 -->
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+## References
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+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
CADPS2.md
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## History
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Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
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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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+ 2021-05-05 : Hübschmann : DLBCL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
SOCS1.md
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# SOCS1
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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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+ 2006-04-27 : Weniger : PMBL
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+ 2011-07-27 : Morin : DLBCL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
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<!-- ORIGIN: wenigerMutationsTumorSuppressor2006a -->
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<!-- PMBL: wenigerMutationsTumorSuppressor2006a -->
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<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
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+## References
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+1. Weniger MA, Melzner I, Menz CK, Wegener S, Bucur AJ, Dorsch K, Mattfeldt T, Barth TFE, Möller P. Mutations of the tumor suppressor gene SOCS-1 in classical Hodgkin lymphoma are frequent and associated with nuclear phospho-STAT5 accumulation. Oncogene. 2006 Apr 27;25(18):2679–2684. PMID: 16532038
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+2. 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