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A user guide for the online exploration and visualization of PCAWG data.

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dc.contributor.authorGoldman, Mary J
dc.contributor.authorZhang, Junjun
dc.contributor.authorFonseca, Nuno A
dc.contributor.authorCortés-Ciriano, Isidro
dc.contributor.authorXiang, Qian
dc.contributor.authorCraft, Brian
dc.contributor.authorPiñeiro-Yáñez, Elena
dc.contributor.authorO'Connor, Brian D
dc.contributor.authorBazant, Wojciech
dc.contributor.authorBarrera, Elisabet
dc.contributor.authorMuñoz-Pomer, Alfonso
dc.contributor.authorPetryszak, Robert
dc.contributor.authorFüllgrabe, Anja
dc.contributor.authorAl-Shahrour, Fatima
dc.contributor.authorKeays, Maria
dc.contributor.authorHaussler, David
dc.contributor.authorWeinstein, John N
dc.contributor.authorHuber, Wolfgang
dc.contributor.authorValencia, Alfonso
dc.contributor.authorPark, Peter J
dc.contributor.authorPapatheodorou, Irene
dc.contributor.authorZhu, Jingchun
dc.contributor.authorFerretti, Vincent
dc.contributor.authorVazquez, Miguel
dc.contributor.funderUnión Europea
dc.contributor.funderUnión Europea. Comisión Europea. European Research Council (ERC)
dc.contributor.funderEuropean Molecular Biology Laboratory
dc.contributor.funderNIH - National Cancer Institute (NCI) (Estados Unidos)
dc.date.accessioned2020-07-13T11:12:42Z
dc.date.available2020-07-13T11:12:42Z
dc.date.issued2020-07-07
dc.description.abstractThe Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user's guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, and demonstrate how the tools can be used together to understand the biology of cancers more deeply. Together, the tools enable researchers to query the complex genomic PCAWG data dynamically and integrate external information, enabling and enhancing interpretation.es_ES
dc.description.peerreviewedSíes_ES
dc.description.sponsorshipThe ICGC Data Portal development is supported by the Ontario Institute for Cancer Research (OICR) through funding provided by the government of Ontario. UCSC Xena development is supported by the National Cancer Institute of the National Institutes of Health under award numbers 5U24CA180951-04 and 5U24CA210974-02. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Chromothripsis Explorer development is supported by the European Union’s Framework Programme For Research and Innovation Horizon 2020 (2014-2020) under the Marie Curie Sklodowska-Curie Grant Agreement No. 703543 (I.C.-C.). Expression Atlas development is supported by the European Molecular Biology Laboratory (EMBL) member states, the Single Cell Gene Expression Atlas from the Wellcome Trust (grant numbers 108437/Z/15/Z), the National Science Foundation of USA grant to Gramene database [NSF IOS #1127112], Open Targets, and Chan Zuckerberg Initiative. PCAWG-Scout development is supported by joint BSC-IRB-CRG Program in Computational Biology and Severo Ochoa Award SEV 2015-0493. In addition, this work has been supported by the Spanish Government (SEV 2015-0493) and from the BSC-Lenovo Master Collaboration Agreement (2015). We acknowledge the contributions of the many clinical networks across ICGC and TCGA who provided samples and data to the PCAWG Consortium and the contributions of the Technical Working Group and the Germline Working Group of the PCAWG Consortium for collation, realignment, and harmonized variant calling of the cancer genomes used in this study. We thank the patients and their families for their participation in the individual ICGC and TCGA projects.
dc.format.number1es_ES
dc.format.page3400es_ES
dc.format.volume11es_ES
dc.identifier.citationNat Commun. 2020;11(1):3400.es_ES
dc.identifier.doi10.1038/s41467-020-16785-6es_ES
dc.identifier.e-issn2041-1723es_ES
dc.identifier.journalNature communicationses_ES
dc.identifier.pubmedID32636365es_ES
dc.identifier.urihttp://hdl.handle.net/20.500.12105/10744
dc.language.isoenges_ES
dc.publisherNature Publishing Group
dc.relation.projectIDinfo:eu_repo/grantAgreement/EC/H2020/703543es_ES
dc.relation.projectIDinfo:eu_repo/grantAgreement/ES/SEV 2015-0493es_ES
dc.relation.publisherversionhttps://doi.org/ 10.1038/s41467-020-16785-6.es_ES
dc.repisalud.institucionCNIOes_ES
dc.repisalud.orgCNIOCNIO::Unidades técnicas::Unidad de Bioinformáticaes_ES
dc.rights.accessRightsopen accesses_ES
dc.rights.licenseAtribución-NoComercial-CompartirIgual 4.0 Internacional*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.titleA user guide for the online exploration and visualization of PCAWG data.es_ES
dc.typejournal articlees_ES
dc.type.hasVersionVoRes_ES
dspace.entity.typePublication
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