A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Alioto, Tyler S., Buchhalter, Ivo, Derdak, Sophia, Hutter, Barbara, Eldridge, Matthew D., Hovig, Eivind, Heisler, Lawrence E., Beck, Timothy A., Simpson, Jared T., Tonon, Laurie, Sertier, Anne-Sophie, Patch, Ann-Marie, Jager, Natalie, Ginsbach, Philip, Drews, Ruben, Paramasivam, Nagarajan, Kabbe, Rolf, Chotewutmontri, Sasithorn, Diessl, Nicolle, Previti, Christopher, Schmidt, Sabine, Brors, Benedikt, Feuerbach, Lars, Heinold, Michael, Grobner, Susanne, Korshunov, Andrey, Tarpey, Patrick S., Butler, Adam P., Hinton, Jonathan, Jones, David, Menzies, Andrew, Raine, Keiran, Shepherd, Rebecca, Stebbings, Lucy, Teague, Jon W., Ribeca, Paolo, Giner, Francesc, Beltran, Sergi, Raineri, Emanuele, Dabad, Marc, Heath, Simon C., Gut, Marta, Denroche, Robert E., Harding, Nicholas J., Yamaguchi, Takafumi N., Fujimoto, Akihiro, Nakagawa, Hidewaki, Quesada, Victor, Valdes-Mas, Rafael, Nakken, Sigve, Vodak, Daniel, Bower, Lawrence, Lynch, Andrew G., Anderson, Charlotte L., Waddell, Nicola, Pearson, John V., Grimmond, Sean M., Peto, Myron, Spellman, Paul, He, Minghui, Kandoth, Cyriac, Lee, Semin, Zhang, John, Letourneau, Louis, Ma, Singer, Seth, Sahil, Torrents, David, Xi, Liu, Wheeler, David A., Lopez-Otin, Carlos, Campo, Elias, Campbell, Peter J., Boutros, Paul C., Puente, Xose S., Gerhard, Daniela S., Pfister, Stefan M., McPherson, John D., Hudson, Thomas J., Schlesner, Matthias, Lichter, Peter, Eils, Roland, Jones, David T.W. and Gut, Ivo G. (2015) A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications, 6 10001: . doi:10.1038/ncomms10001

Author Alioto, Tyler S.
Buchhalter, Ivo
Derdak, Sophia
Hutter, Barbara
Eldridge, Matthew D.
Hovig, Eivind
Heisler, Lawrence E.
Beck, Timothy A.
Simpson, Jared T.
Tonon, Laurie
Sertier, Anne-Sophie
Patch, Ann-Marie
Jager, Natalie
Ginsbach, Philip
Drews, Ruben
Paramasivam, Nagarajan
Kabbe, Rolf
Chotewutmontri, Sasithorn
Diessl, Nicolle
Previti, Christopher
Schmidt, Sabine
Brors, Benedikt
Feuerbach, Lars
Heinold, Michael
Grobner, Susanne
Korshunov, Andrey
Tarpey, Patrick S.
Butler, Adam P.
Hinton, Jonathan
Jones, David
Menzies, Andrew
Raine, Keiran
Shepherd, Rebecca
Stebbings, Lucy
Teague, Jon W.
Ribeca, Paolo
Giner, Francesc
Beltran, Sergi
Raineri, Emanuele
Dabad, Marc
Heath, Simon C.
Gut, Marta
Denroche, Robert E.
Harding, Nicholas J.
Yamaguchi, Takafumi N.
Fujimoto, Akihiro
Nakagawa, Hidewaki
Quesada, Victor
Valdes-Mas, Rafael
Nakken, Sigve
Vodak, Daniel
Bower, Lawrence
Lynch, Andrew G.
Anderson, Charlotte L.
Waddell, Nicola
Pearson, John V.
Grimmond, Sean M.
Peto, Myron
Spellman, Paul
He, Minghui
Kandoth, Cyriac
Lee, Semin
Zhang, John
Letourneau, Louis
Ma, Singer
Seth, Sahil
Torrents, David
Xi, Liu
Wheeler, David A.
Lopez-Otin, Carlos
Campo, Elias
Campbell, Peter J.
Boutros, Paul C.
Puente, Xose S.
Gerhard, Daniela S.
Pfister, Stefan M.
McPherson, John D.
Hudson, Thomas J.
Schlesner, Matthias
Lichter, Peter
Eils, Roland
Jones, David T.W.
Gut, Ivo G.
Title A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
Journal name Nature Communications   Check publisher's open access policy
ISSN 2041-1723
Publication date 2015-12-09
Year available 2015
Sub-type Article (original research)
DOI 10.1038/ncomms10001
Open Access Status DOI
Volume 6
Issue 10001
Total pages 13
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Subject 1600 Chemistry
1300 Biochemistry, Genetics and Molecular Biology
3100 Physics and Astronomy
Abstract 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2016 Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 55 times in Thomson Reuters Web of Science Article | Citations
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