Journal Article

DKFZ-2020-02167

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Framework for quality assessment of whole genome cancer sequences.

Whalley, J. P. ; Buchhalter, I.DKFZ* ; Rheinbay, E. ; Raine, K. M. ; Stobbe, M. D. ; Kleinheinz, K.DKFZ* ; Werner, J. ; Beltran, S. ; Gut, M. ; Hübschmann, D.DKFZ* ; Hutter, B.DKFZ* ; Livitz, D. ; Perry, M. D. ; Rosenberg, M. ; Saksena, G. ; Trotta, J.-R. ; Eils, R. ; Gerhard, D. S. ; Campbell, P. J. ; Schlesner, M.DKFZ* ; Gut, I. G.

2020
Nature Publishing Group UK [London]

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Please use a persistent id in citations: doi:10.1038/s41467-020-18688-y

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 .

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Contributing Institute(s):

1. Theoretische Bioinformatik (B080)
2. Core Facility Omics IT (W610)
3. Angewandte Bioinformatik (G200)
4. Angewandte Bioinformatik (B330)
5. Bioinformatik und Omics Data Analytics (B240)

Research Program(s):

1. 312 - Functional and structural genomics (POF3-312) (POF3-312)

Appears in the scientific report 2020

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