TY  - JOUR
AU  - Alioto, Tyler S
AU  - Buchhalter, Ivo
AU  - Derdak, Sophia
AU  - Hutter, Barbara
AU  - Eldridge, Matthew D
AU  - Hovig, Eivind
AU  - Heisler, Lawrence E
AU  - Beck, Timothy A
AU  - Simpson, Jared T
AU  - Tonon, Laurie
AU  - Sertier, Anne-Sophie
AU  - Patch, Ann-Marie
AU  - Jäger, Natalie
AU  - Ginsbach, Philip
AU  - Drews, Ruben
AU  - Paramasivam, Nagarajan
AU  - Kabbe, Rolf
AU  - Chotewutmontri, Sasithorn
AU  - Diessl, Nicolle
AU  - Previti, Christopher
AU  - Schmidt, Sabine
AU  - Brors, Benedikt
AU  - Feuerbach, Lars
AU  - Heinold, Michael
AU  - Gröbner, Susanne
AU  - Korshunov, Andrey
AU  - Tarpey, Patrick S
AU  - Butler, Adam P
AU  - Hinton, Jonathan
AU  - Jones, David
AU  - Menzies, Andrew
AU  - Raine, Keiran
AU  - Shepherd, Rebecca
AU  - Stebbings, Lucy
AU  - Teague, Jon W
AU  - Ribeca, Paolo
AU  - Giner, Francesc Castro
AU  - Beltran, Sergi
AU  - Raineri, Emanuele
AU  - Dabad, Marc
AU  - Heath, Simon C
AU  - Gut, Marta
AU  - Denroche, Robert E
AU  - Harding, Nicholas J
AU  - Yamaguchi, Takafumi N
AU  - Fujimoto, Akihiro
AU  - Nakagawa, Hidewaki
AU  - Quesada, Víctor
AU  - Valdés-Mas, Rafael
AU  - Nakken, Sigve
AU  - Vodák, Daniel
AU  - Bower, Lawrence
AU  - Lynch, Andrew G
AU  - Anderson, Charlotte L
AU  - Waddell, Nicola
AU  - Pearson, John V
AU  - Grimmond, Sean M
AU  - Peto, Myron
AU  - Spellman, Paul
AU  - He, Minghui
AU  - Kandoth, Cyriac
AU  - Lee, Semin
AU  - Zhang, John
AU  - Létourneau, Louis
AU  - Ma, Singer
AU  - Seth, Sahil
AU  - Torrents, David
AU  - Xi, Liu
AU  - Wheeler, David A
AU  - López-Otín, Carlos
AU  - Campo, Elías
AU  - Campbell, Peter J
AU  - Boutros, Paul C
AU  - Puente, Xose S
AU  - Gerhard, Daniela S
AU  - Pfister, Stefan
AU  - McPherson, John D
AU  - Hudson, Thomas J
AU  - Schlesner, Matthias
AU  - Lichter, Peter
AU  - Eils, Roland
AU  - Jones, David
AU  - Gut, Ivo G
TI  - A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.
JO  - Nature Communications
VL  - 6
SN  - 2041-1723
CY  - London
PB  - Nature Publishing Group
M1  - DKFZ-2017-02148
SP  - 10001
PY  - 2015
AB  - As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.
LB  - PUB:(DE-HGF)16
C6  - pmid:26647970
C2  - pmc:PMC4682041
DO  - DOI:10.1038/ncomms10001
UR  - https://inrepo02.dkfz.de/record/126033
ER  -