Framework for quality assessment of whole genome cancer sequences

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 ()
Additional contact information
Justin P. Whalley: Barcelona Institute of Science and Technology (BIST)
Ivo Buchhalter: German Cancer Research Centre (DKFZ)
Esther Rheinbay: Broad Institute of Harvard and MIT
Keiran M. Raine: Wellcome Sanger Institute
Miranda D. Stobbe: Barcelona Institute of Science and Technology (BIST)
Kortine Kleinheinz: German Cancer Research Centre (DKFZ)
Johannes Werner: German Cancer Research Centre (DKFZ)
Sergi Beltran: Barcelona Institute of Science and Technology (BIST)
Marta Gut: Barcelona Institute of Science and Technology (BIST)
Daniel Hübschmann: German Cancer Research Centre (DKFZ)
Barbara Hutter: Cancer Research Centre (DKFZ)
Dimitri Livitz: Broad Institute of Harvard and MIT
Marc D. Perry: University of California
Mara Rosenberg: Broad Institute of Harvard and MIT
Gordon Saksena: Broad Institute of Harvard and MIT
Jean-Rémi Trotta: Barcelona Institute of Science and Technology (BIST)
Roland Eils: Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin
Daniela S. Gerhard: National Cancer Institute, US National Institutes of Health
Peter J. Campbell: Wellcome Sanger Institute
Matthias Schlesner: German Cancer Research Centre (DKFZ)
Ivo G. Gut: Barcelona Institute of Science and Technology (BIST)

Nature Communications, 2020, vol. 11, issue 1, 1-8

Abstract: 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 .

Date: 2020
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DOI: 10.1038/s41467-020-18688-y

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