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Framework for quality assessment of whole genome cancer sequences

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....

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Main Authors: Whalley, Justin P. (Author) , Buchhalter, Ivo (Author) , Rheinbay, Esther (Author) , Raine, Keiran M. (Author) , Stobbe, Miranda D. (Author) , Kleinheinz, Kortine (Author) , Werner, Johannes (Author) , Beltran, Sergi (Author) , Gut, Marta (Author) , Hübschmann, Daniel (Author) , Hutter, Barbara (Author) , Livitz, Dimitri (Author) , Perry, Marc D. (Author) , Rosenberg, Mara (Author) , Saksena, Gordon (Author) , Trotta, Jean-Rémi (Author) , Eils, Roland (Author) , Gerhard, Daniela S. (Author) , Campbell, Peter J. (Author) , Schlesner, Matthias (Author) , Gut, Ivo G. (Author)
Format: Article (Journal)
Language:English
Published: 07 October 2020
In: Nature Communications
Year: 2020, Volume: 11
ISSN:2041-1723
DOI:10.1038/s41467-020-18688-y
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41467-020-18688-y
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41467-020-18688-y
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Author Notes:Justin P. Whalley, Ivo Buchhalter, Esther Rheinbay, Keiran M. Raine, Miranda D. Stobbe, Kortine Kleinheinz, Johannes Werner, Sergi Beltran, Marta Gut, Daniel Hübschmann, Barbara Hutter, Dimitri Livitz, Marc D. Perry, Mara Rosenberg, Gordon Saksena, Jean-Rémi Trotta, Roland Eils, Daniela S. Gerhard, Peter J. Campbell, Matthias Schlesner and Ivo G. Gut
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Summary: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.
Item Description:Gesehen am 16.11.2020
Physical Description:Online Resource
ISSN:2041-1723
DOI:10.1038/s41467-020-18688-y

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