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dc.contributor.authorNadeu, Ferran
dc.contributor.authorMas-de-les-Valls, Rut
dc.contributor.authorNavarro, Alba
dc.contributor.authorRoyo, Romina
dc.contributor.authorMartín, Silvia
dc.contributor.authorVillamor, Neus
dc.contributor.authorSuárez-Cisneros, Helena
dc.contributor.authorMares, Rosó
dc.contributor.authorLu, Junyan
dc.contributor.authorEnjuanes, Anna
dc.contributor.authorRivas-Delgado, Alfredo
dc.contributor.authorAymerich, Marta
dc.contributor.authorBaumann, Tycho
dc.contributor.authorColomer, Dolors
dc.contributor.authorDelgado, Julio
dc.contributor.authorMorin, Ryan D.
dc.contributor.authorZenz, Thorsten
dc.contributor.authorPuente, Xose S.
dc.contributor.authorCampbell, Peter J.
dc.contributor.authorBeà, Sílvia
dc.contributor.authorMaura, Francesco
dc.contributor.authorCampo, Elías
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2020-09-04T10:25:12Z
dc.date.available2020-09-04T10:25:12Z
dc.date.issued2020-07
dc.identifier.citationNadeu, F. [et al.]. IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms. "Nature Communications", Juliol 2020, vol. 11, 3390.
dc.identifier.issn2041-1723
dc.identifier.urihttp://hdl.handle.net/2117/328399
dc.description.abstractImmunoglobulin (Ig) gene rearrangements and oncogenic translocations are routinely assessed during the characterization of B cell neoplasms and stratification of patients with distinct clinical and biological features, with the assessment done using Sanger sequencing, targeted next-generation sequencing, or fluorescence in situ hybridization (FISH). Currently, a complete Ig characterization cannot be extracted from whole-genome sequencing (WGS) data due to the inherent complexity of the Ig loci. Here, we introduce IgCaller, an algorithm designed to fully characterize Ig gene rearrangements and oncogenic translocations from short-read WGS data. Using a cohort of 404 patients comprising different subtypes of B cell neoplasms, we demonstrate that IgCaller identifies both heavy and light chain rearrangements to provide additional information on their functionality, somatic mutational status, class switch recombination, and oncogenic Ig translocations. Our data thus support IgCaller to be a reliable alternative to Sanger sequencing and FISH for studying the genetic properties of the Ig loci.
dc.description.sponsorshipWe are indebted to the Genomics Core Facility of the Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) for the technical support, to R. Siebert and D. Huebschmann for sharing the CSR regions, and to K. Stamatopoulos, E. Vlachonikola and F. Psomopoulos for their helpful comments on the manuscript. We thank R. Eils, P. Lichter, C. von Kalle, S. Fröhling, H. Glimm, M. Zapatka, S. Wolf, K. Beck, and J. Kirchhof for infrastructure and pipeline development within DKFZ-HIPO and NCT POP. This study was supported by the Instituto de Salud Carlos III and the European Regional Development Fund “Una manera de hacer Europa” (PMP15/00007 to E.C.), the “la Caixa” Foundation (CLLEvolution-LCF/PR/HR17/52150017, Health Research 2017 Program HR17-00221 to E.C.), the National Institute of Health “Molecular Diagnosis, Prognosis, and Therapeutic Targets in Mantle Cell Lymphoma” (P01CA229100 to E.C.), and CERCA Programme/Generalitat de Catalunya. F.N. is supported by a pre-doctoral fellowship of the Ministerio de Economía y Competitividad (BES-2016-076372). F.M. is supported by the Memorial Sloan Kettering Cancer Center NCI Core Grant (P30 CA 008748). E.C. is an Academia Researcher of the “Institució Catalana de Recerca i Estudis Avançats” (ICREA) of the Generalitat de Catalunya. This work was partially developed at the Centre Esther Koplowitz (CEK, Barcelona, Spain).
dc.format.extent11 p.
dc.language.isoeng
dc.publisherSpringer Nature
dc.rightsAttribution 3.0 Spain
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/es/
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subject.lcshGenomics
dc.subject.lcshCancer--Genetic aspects
dc.subject.lcshImmunoglobulin genes
dc.subject.otherHaematological cancer
dc.subject.otherCancer genomics
dc.subject.otherImmunogenetics
dc.subject.otherIgCaller
dc.subject.otherIg gene rearrangements
dc.titleIgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms
dc.typeArticle
dc.subject.lemacGenòmica -- Informàtica
dc.subject.lemacGenòmica
dc.identifier.doi10.1038/s41467-020-17095-7
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttps://www.nature.com/articles/s41467-020-17095-7
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
local.citation.other3390
local.citation.publicationNameNature Communications
local.citation.volume11
dc.relation.datasethttps://ega-archive.org/studies/EGAS00001001306
dc.relation.datasethttps://ega-archive.org/studies/EGAS00001000510
dc.relation.datasethttps://ega-archive.org/studies/EGAS00001001299
dc.relation.datasethttps://ega-archive.org/studies/EGAS00001002936


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Attribution 3.0 Spain
Except where otherwise noted, content on this work is licensed under a Creative Commons license : Attribution 3.0 Spain