{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T01:17:22Z","timestamp":1781918242966,"version":"3.54.5"},"reference-count":90,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T00:00:00Z","timestamp":1620086400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fundaci\u00f3n Galega de Hematolox\u00eda e Hemoterapia"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>B-cell lymphoproliferative disorders exhibit a diverse spectrum of diagnostic entities with heterogeneous behaviour. Multiple efforts have focused on the determination of the genomic drivers of B-cell lymphoma subtypes. In the meantime, the aggregation of diverse tumors in pan-cancer genomic studies has become a useful tool to detect new driver genes, while enabling the comparison of mutational patterns across tumors. Here we present an integrated analysis of 354 B-cell lymphoid disorders. 112 recurrently mutated genes were discovered, of which<jats:italic>KMT2D<\/jats:italic>,<jats:italic>CREBBP<\/jats:italic>,<jats:italic>IGLL5<\/jats:italic>and<jats:italic>BCL2<\/jats:italic>were the most frequent, and 31 genes were putative new drivers. Mutations in<jats:italic>CREBBP<\/jats:italic>,<jats:italic>TNFRSF14<\/jats:italic>and<jats:italic>KMT2D<\/jats:italic>predominated in follicular lymphoma, whereas those in<jats:italic>BTG2<\/jats:italic>,<jats:italic>HTA-A<\/jats:italic>and<jats:italic>PIM1<\/jats:italic>were more frequent in diffuse large B-cell lymphoma. Additionally, we discovered 31 significantly mutated protein networks, reinforcing the role of genes such as<jats:italic>CREBBP<\/jats:italic>,<jats:italic>EEF1A1<\/jats:italic>,<jats:italic>STAT6<\/jats:italic>,<jats:italic>GNA13<\/jats:italic>and<jats:italic>TP53<\/jats:italic>, but also pointing towards a myriad of infrequent players in lymphomagenesis. Finally, we report aberrant expression of oncogenes and tumor suppressors associated with novel noncoding mutations (<jats:italic>DTX1<\/jats:italic>and<jats:italic>S1PR2<\/jats:italic>), and new recurrent copy number aberrations affecting immune check-point regulators (<jats:italic>CD83<\/jats:italic>,<jats:italic>PVR<\/jats:italic>) and B-cell specific genes (<jats:italic>TNFRSF13C<\/jats:italic>). Our analysis expands the number of mutational drivers of B-cell lymphoid neoplasms, and identifies several differential somatic events between disease subtypes.<\/jats:p>","DOI":"10.1371\/journal.pone.0248886","type":"journal-article","created":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T19:33:40Z","timestamp":1620156820000},"page":"e0248886","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4838-6750","authenticated-orcid":true,"given":"Adri\u00e1n","family":"Mosquera Orgueira","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roi","family":"Ferreiro 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Alizadeh","year":"2000","journal-title":"Nature"},{"issue":"5","key":"pone.0248886.ref003","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41591-018-0016-8","article-title":"Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes","volume":"24","author":"B Chapuy","year":"2018","journal-title":"Nat Med"},{"issue":"15","key":"pone.0248886.ref004","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1056\/NEJMoa1801445","article-title":"Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma","volume":"378","author":"R Schmitz","year":"2018","journal-title":"N Engl J Med"},{"issue":"2","key":"pone.0248886.ref005","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/leu.2014.209","article-title":"Genomic and epigenomic co-evolution in follicular lymphomas","volume":"29","author":"M Loeffler","year":"2015","journal-title":"Leukemia"},{"issue":"9","key":"pone.0248886.ref006","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/S1470-2045(15)00169-2","article-title":"Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma: a retrospective analysis of a prospective clinical trial and validation in a population-based registry","volume":"16","author":"A Pastore","year":"2015","journal-title":"Lancet Oncol"},{"issue":"7574","key":"pone.0248886.ref007","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nature15395","article-title":"Mutations driving CLL and their evolution in progression and relapse","volume":"526","author":"DA Landau","year":"2015","journal-title":"Nature"},{"issue":"7574","key":"pone.0248886.ref008","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nature14666","article-title":"Non-coding recurrent mutations in chronic lymphocytic 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Batmanov","year":"2017","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0248886.ref015","doi-asserted-by":"crossref","first-page":"4001","DOI":"10.1038\/s41467-018-06354-3","article-title":"Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma","volume":"9","author":"SE Arthur","year":"2018","journal-title":"Nat Commun"},{"key":"pone.0248886.ref016","doi-asserted-by":"crossref","first-page":"43169","DOI":"10.1038\/srep43169","article-title":"Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data","volume":"7","author":"S Sandmann","year":"2017","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0248886.ref017","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s12859-016-1417-7","article-title":"Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers","volume":"18","author":"AL Hofmann","year":"2017","journal-title":"BMC 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Priestley","year":"2019","journal-title":"Nature"},{"issue":"7696","key":"pone.0248886.ref021","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nature25795","article-title":"Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours","volume":"555","author":"X Ma","year":"2018","journal-title":"Nature"},{"issue":"10","key":"pone.0248886.ref022","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The Cancer Genome Atlas Pan-Cancer analysis project","volume":"45","author":"Cancer Genome Atlas Research Network","year":"2013","journal-title":"Nat Genet"},{"key":"pone.0248886.ref023","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"International Cancer Genome Consortium","year":"2010","journal-title":"Nature"},{"key":"pone.0248886.ref024","doi-asserted-by":"crossref","first-page":"30","DOI":"10.14806\/ej.17.B.286","article-title":"Bcbio-nextgen: Automated, distributed, next-gen sequencing pipeline","volume":"17","author":"R. Valls-Guimera","year":"2012","journal-title":"EMBnet journal"},{"key":"pone.0248886.ref025","doi-asserted-by":"crossref","first-page":"e108","DOI":"10.1093\/nar\/gkw227","article-title":"VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research","volume":"44","author":"Z Lai","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pone.0248886.ref026","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"DC Koboldt","year":"2012","journal-title":"Genome Res"},{"key":"pone.0248886.ref027","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1186\/s12859-016-1190-7","article-title":"Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data","volume":"17","author":"IF do Valle","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"pone.0248886.ref028","unstructured":"Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv, 1207.3907 [q-bio.GN] (2012)"},{"key":"pone.0248886.ref029","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"1000 Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"pone.0248886.ref030","doi-asserted-by":"crossref","unstructured":"Karczewski, K.J. et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv 531210, https:\/\/doi.org\/10.1101\/531210","DOI":"10.1101\/531210"},{"key":"pone.0248886.ref031","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"M Lek","year":"2016","journal-title":"Nature"},{"issue":"4","key":"pone.0248886.ref032","doi-asserted-by":"crossref","first-page":"e1004873","DOI":"10.1371\/journal.pcbi.1004873","article-title":"CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing","volume":"12","author":"E Talevich","year":"2016","journal-title":"PLoS Comput Biol"},{"issue":"7457","key":"pone.0248886.ref033","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature12213","article-title":"Mutational heterogeneity in cancer and the search for new cancer-associated genes","volume":"499","author":"MS Lawrence","year":"2013","journal-title":"Nature"},{"issue":"5","key":"pone.0248886.ref034","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2017.09.042","article-title":"Universal Patterns of Selection in Cancer and Somatic Tissues","volume":"171","author":"I Martincorena","year":"2017","journal-title":"Cell"},{"issue":"1","key":"pone.0248886.ref035","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s13059-016-0994-0","article-title":"OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations","volume":"17","author":"L Mularoni","year":"2016","journal-title":"Genome Biol"},{"issue":"17","key":"pone.0248886.ref036","doi-asserted-by":"crossref","first-page":"i972","DOI":"10.1093\/bioinformatics\/bty613","article-title":"Hierarchical HotNet: identifying hierarchies of altered subnetworks","volume":"34","author":"MA Reyna","year":"2018","journal-title":"Bioinformatics"},{"key":"pone.0248886.ref037","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for The ENCODE Project","volume":"22","author":"J Harrow","year":"2012","journal-title":"Genome Res"},{"key":"pone.0248886.ref038","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","author":"S Fishilevich","year":"2017","journal-title":"Database (Oxford)"},{"key":"pone.0248886.ref039","doi-asserted-by":"crossref","first-page":"8123","DOI":"10.1093\/nar\/gkv803","article-title":"LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations","volume":"43","author":"L Lochovsky","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"pone.0248886.ref040","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.18632\/oncotarget.653","article-title":"Recurrent targets of aberrant somatic hypermutation in lymphoma","volume":"3","author":"AH Khodabakhshi","year":"2012","journal-title":"Oncotarget"},{"issue":"7","key":"pone.0248886.ref041","doi-asserted-by":"crossref","first-page":"e40332","DOI":"10.1371\/journal.pone.0040332","article-title":"Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma","volume":"7","author":"Y Jiang","year":"2012","journal-title":"PLoS One"},{"issue":"6","key":"pone.0248886.ref042","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1007\/s00401-016-1536-2","article-title":"Genomic characterization of primary central nervous system lymphoma","volume":"131","author":"K Fukumura","year":"2016","journal-title":"Acta Neuropathol"},{"issue":"2","key":"pone.0248886.ref043","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s43018-020-0027-5","article-title":"A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies","volume":"1","author":"A Degasperi","year":"2020","journal-title":"Nat Cancer"},{"issue":"4","key":"pone.0248886.ref044","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"CH Mermel","year":"2011","journal-title":"Genome Biol"},{"issue":"5","key":"pone.0248886.ref045","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v027.i05","article-title":"Nonparametric Econometrics: The np Package","volume":"27","author":"T Hayfield","year":"2008","journal-title":"Journal of Statistical Software"},{"issue":"W1","key":"pone.0248886.ref046","doi-asserted-by":"crossref","first-page":"W199","DOI":"10.1093\/nar\/gkz401","article-title":"WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs","volume":"47","author":"Y Liao","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"pone.0248886.ref047","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1182\/bloodadvances.2018016162","article-title":"Interplay between HGAL and Grb2 proteins regulates B-cell receptor signaling","volume":"3","author":"X Jiang","year":"2019","journal-title":"Blood Adv"},{"issue":"7552","key":"pone.0248886.ref048","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nature14231","article-title":"Signalling thresholds and negative B-cell selection in acute lymphoblastic leukaemia","volume":"521","author":"Z Chen","year":"2015","journal-title":"Nature"},{"issue":"3","key":"pone.0248886.ref049","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1002\/mc.22938","article-title":"Lymphotoxin-\u03b2 receptor-NIK signaling induces alternative RELB\/NF-\u03baB2 activation to promote metastatic gene expression and cell migration in head and neck cancer","volume":"58","author":"R Das","year":"2019","journal-title":"Mol Carcinog"},{"issue":"5","key":"pone.0248886.ref050","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1016\/j.celrep.2018.01.013","article-title":"TRAF6 Mediates Basal Activation of NF-\u03baB Necessary for Hematopoietic Stem Cell Homeostasis","volume":"22","author":"J Fang","year":"2018","journal-title":"Cell Rep"},{"issue":"7","key":"pone.0248886.ref051","doi-asserted-by":"crossref","first-page":"2170","DOI":"10.1002\/art.22727","article-title":"Angiopoietin 1 directly induces destruction of the rheumatoid joint by cooperative, but independent, signaling via ERK\/MAPK and phosphatidylinositol 3-kinase\/","volume":"56","author":"A Hashiramoto","year":"2007","journal-title":"Akt. Arthritis Rheum"},{"issue":"2","key":"pone.0248886.ref052","first-page":"159","article-title":"Down-Regulation of Ribosomal S6 kinase RPS6KA6 in Acute Myeloid Leukemia Patients","volume":"18","author":"M Rafiee","year":"2016","journal-title":"Cell J"},{"issue":"1","key":"pone.0248886.ref053","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1038\/s41467-019-09180-3","article-title":"PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice","volume":"10","author":"J Weber","year":"2019","journal-title":"Nat Commun"},{"issue":"1","key":"pone.0248886.ref054","doi-asserted-by":"crossref","first-page":"2742","DOI":"10.1038\/s41598-018-21160-z","article-title":"ZFP36L1 and ZFP36L2 inhibit cell proliferation in a cyclin D-dependent and p53-independent manner","volume":"8","author":"FM Suk","year":"2018","journal-title":"Sci 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Rohde","year":"2017","journal-title":"Haematologica"},{"key":"pone.0248886.ref058","article-title":"IRF4-rearranged Large B-cell lymphoma (LBCL) has a genomic profile distinct to other LBCL in children and young adults","author":"JE Ramis-Zaldivar","year":"2019","journal-title":"Blood"},{"issue":"9","key":"pone.0248886.ref059","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1084\/jem.20120904","article-title":"The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development","volume":"209","author":"D Rossi","year":"2012","journal-title":"J Exp Med"},{"issue":"5","key":"pone.0248886.ref060","doi-asserted-by":"crossref","first-page":"e195","DOI":"10.3324\/haematol.2016.157495","article-title":"Deltex-1 mutations predict poor survival in diffuse large B-cell lymphoma","volume":"102","author":"L Meriranta","year":"2017","journal-title":"Haematologica"},{"issue":"20","key":"pone.0248886.ref061","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1182\/blood-2017-10-810630","article-title":"The tumor suppressive TGF-\u03b2\/SMAD1\/S1PR2 signaling axis is recurrently inactivated in diffuse large B-cell lymphoma","volume":"131","author":"A Stelling","year":"2018","journal-title":"Blood"},{"issue":"1","key":"pone.0248886.ref062","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/leu.2016.175","article-title":"Combined copy number and mutation analysis identifies oncogenic pathways associated with transformation of follicular lymphoma","volume":"31","author":"A Bouska","year":"2017","journal-title":"Leukemia"},{"issue":"4","key":"pone.0248886.ref063","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1111\/j.1365-2141.2004.05226.x","article-title":"Role of CD21 antigen in diffuse large B-cell lymphoma and its clinical 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Balint","year":"2016","journal-title":"Int J Mol Sci"},{"issue":"8","key":"pone.0248886.ref067","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1038\/leu.2015.57","article-title":"IL10 receptor is a novel therapeutic target in DLBCLs","volume":"29","author":"W B\u00e9guelin","year":"2015","journal-title":"Leukemia"},{"issue":"4","key":"pone.0248886.ref068","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1016\/j.bbrc.2018.08.030","article-title":"IL-13 and IL-13R\u03b11 are overexpressed in extranodal natural killer\/T cell lymphoma and mediate tumor cell proliferation","volume":"503","author":"Y Zhang","year":"2018","journal-title":"Biochem Biophys Res Commun"},{"issue":"25","key":"pone.0248886.ref069","doi-asserted-by":"crossref","first-page":"3301","DOI":"10.1038\/sj.onc.1204421","article-title":"Mutations in the mitotic check point gene, MAD1L1, in human cancers","volume":"20","author":"K 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Pinyol","year":"1998","journal-title":"Blood"},{"issue":"2","key":"pone.0248886.ref076","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/S0165-4608(98)00138-1","article-title":"Deletion of cell division cycle 2-like 1 gene locus on 1p36 in non-Hodgkin lymphoma","volume":"108","author":"BJ Dave","year":"1999","journal-title":"Cancer Genet Cytogenet"},{"issue":"5","key":"pone.0248886.ref077","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1002\/ijc.29072","article-title":"Characterization of genomic imbalances in diffuse large B-cell lymphoma by detailed SNP-chip analysis","volume":"136","author":"R Scholtysik","year":"2015","journal-title":"Int J Cancer"},{"issue":"9","key":"pone.0248886.ref078","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1158\/1541-7786.495.2.9","article-title":"Minimal 16q genomic loss implicates cadherin-11 in retinoblastoma","volume":"2","author":"MN Marchong","year":"2004","journal-title":"Mol Cancer 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