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Framework for quality assessment of whole genome cancer sequences

Author

Listed:
  • Justin P. Whalley

    (Barcelona Institute of Science and Technology (BIST)
    University of Oxford, Roosevelt Drive)

  • Ivo Buchhalter

    (German Cancer Research Centre (DKFZ)
    Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University
    German Cancer Research Center (DKFZ)
    Cancer Research Centre (DKFZ))

  • Esther Rheinbay

    (Broad Institute of Harvard and MIT
    Massachusetts General Hospital Cancer Center and Department of Pathology)

  • 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)
    Leibniz Institute of Baltic Sea Research)

  • 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)
    Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University
    University Hospital Heidelberg
    National Center for Tumor diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ))

  • Barbara Hutter

    (Cancer Research Centre (DKFZ)
    National Center for Tumor diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ))

  • Dimitri Livitz

    (Broad Institute of Harvard and MIT)

  • Marc D. Perry

    (University of California)

  • Mara Rosenberg

    (Broad Institute of Harvard and MIT
    Massachusetts General Hospital Cancer Center and Department of Pathology)

  • 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
    Heidelberg University Hospital and BioQuant)

  • Daniela S. Gerhard

    (National Cancer Institute, US National Institutes of Health)

  • Peter J. Campbell

    (Wellcome Sanger Institute)

  • Matthias Schlesner

    (German Cancer Research Centre (DKFZ)
    German Cancer Research Centre (DKFZ))

  • Ivo G. Gut

    (Barcelona Institute of Science and Technology (BIST)
    Universitat Pompeu Fabra (UPF))

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 .

Suggested Citation

  • 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 & Dim, 2020. "Framework for quality assessment of whole genome cancer sequences," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18688-y
    DOI: 10.1038/s41467-020-18688-y
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