TY  - JOUR
AU  - Whalley, Justin P
AU  - Buchhalter, Ivo
AU  - Rheinbay, Esther
AU  - Raine, Keiran M
AU  - Stobbe, Miranda D
AU  - Kleinheinz, Kortine
AU  - Werner, Johannes
AU  - Beltran, Sergi
AU  - Gut, Marta
AU  - Hübschmann, Daniel
AU  - Hutter, Barbara
AU  - Livitz, Dimitri
AU  - Perry, Marc D
AU  - Rosenberg, Mara
AU  - Saksena, Gordon
AU  - Trotta, Jean-Rémi
AU  - Eils, Roland
AU  - Gerhard, Daniela S
AU  - Campbell, Peter J
AU  - Schlesner, Matthias
AU  - Gut, Ivo G
TI  - Framework for quality assessment of whole genome cancer sequences.
JO  - Nature Communications
VL  - 11
IS  - 1
SN  - 2041-1723
CY  - [London]
PB  - Nature Publishing Group UK
M1  - DKFZ-2020-02167
SP  - 5040
PY  - 2020
AB  - 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 .
LB  - PUB:(DE-HGF)16
C6  - pmid:33028839
DO  - DOI:10.1038/s41467-020-18688-y
UR  - https://inrepo02.dkfz.de/record/163954
ER  -