Framework for quality assessment of whole genome cancer sequences

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  • dc.contributor.author Whalley, Justin P.
  • dc.contributor.author Stobbe, Miranda D.
  • dc.contributor.author Beltran, Sergi
  • dc.contributor.author Gut, Marta
  • dc.contributor.author Trotta, Jean-Remi
  • dc.contributor.author Gut, Ivo Glynne
  • dc.date.accessioned 2020-11-16T06:55:48Z
  • dc.date.available 2020-11-16T06:55:48Z
  • dc.date.issued 2020
  • dc.description.abstract Bringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole genomes sequenced over several years in different sequencing centres requires a framework to compare the quality of these sequences. We used the Pan-Cancer Analysis of Whole Genomes cohort as a test case to construct such a framework. This cohort contains whole cancer genomes of 2832 donors from 18 sequencing centres. We developed a non-redundant set of five quality control (QC) measurements to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses and allow for exclusion of samples of poor quality. We have found that this is an effective framework of quality measures. The implementation of the framework is available at: https://dockstore.org/containers/quay.io/jwerner_dkfz/pancanqc:1.2.2.
  • dc.description.sponsorship J.P.W., M.D.S., S.B., M.G., J.T. and I.G.G. acknowledge the support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the 2014–2020 Smart Growth Operating Program, to the EMBL partnership and co-financing with the European Regional Development Fund (MINECO/FEDER, BIO2015-71792-P). We also acknowledge the support of the Centro de Excelencia Severo Ochoa, and the Generalitat de Catalunya through the Departament de Salut, Departament d’Empresa i Coneixement and the CERCA Programme. We also acknowledge the support through the European Union’s Horizon 2020-funded project EASI-Genomics under grant agreement no 824110. The funding bodies did not have any influence on the design of the study and collection, analysis, and interpretation of data and in writing the paper.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Whalley JP, Buchhalter I, Rheinbay E, Raine KM, Stobbe MD, Kleinheinz K et al. Framework for quality assessment of whole genome cancer sequences. Nat Commun. 2020; 11(1):5040. DOI: 10.1038/s41467-020-18688-y
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-020-18688-y
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/45769
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2020; 11(1):5040
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/824110
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2015-71792-P
  • dc.rights © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Cancer genomics
  • dc.subject.keyword DNA sequencing
  • dc.subject.keyword Research data
  • dc.title Framework for quality assessment of whole genome cancer sequences
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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