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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
W. Xiao, L. Ren, Z. Chen, LT. Fang, Y. Zhao, J. Lack, M. Guan, B. Zhu, E. Jaeger, L. Kerrigan, TM. Blomquist, T. Hung, M. Sultan, K. Idler, C. Lu, A. Scherer, R. Kusko, M. Moos, C. Xiao, ST. Sherry, OD. Abaan, W. Chen, X. Chen, J. Nordlund, U....
Language English Country United States
Document type Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
Grant support
S10OD019960
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
HHSN261201400008C
NCI NIH HHS - United States
HHSN261201500003I
NCI NIH HHS - United States
75N910D00024
NIH HHS - United States
- MeSH
- Benchmarking * MeSH
- Cell Line MeSH
- Humans MeSH
- Mutation MeSH
- Cell Line, Tumor MeSH
- Neoplasms genetics pathology MeSH
- Reproducibility of Results MeSH
- Sequence Analysis, DNA standards MeSH
- Whole Genome Sequencing standards MeSH
- Exome Sequencing standards MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
AstraZeneca Gaithersburg MD USA
Bioinformatics Research and Early Development Roche Sequencing Solutions Inc Belmont CA USA
Biomarker Development Novartis Institutes for Biomedical Research Basel Switzerland
Center for Genomics Loma Linda University School of Medicine Loma Linda CA USA
Center for Information Technology National Institutes of Health Bethesda MD USA
Computational Genomics Genomics Research Center AbbVie North Chicago IL USA
Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA
Departments of Medicine and Pathology University of Toledo Medical Center Toledo OH USA
Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia
European Infrastructure for Translational Medicine Amsterdam the Netherlands
Genentech South San Francisco CA USA
Illumina Inc Foster City CA USA
Immuneering Corporation Cambridge MA USA
IMTM Faculty of Medicine and Dentistry Palacky University Olomouc Olomouc Czech Republic
Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland
Integrative Bioinformatics National Institute of Environmental Health Sciences Durham NC USA
National Center for Toxicological Research US Food and Drug Administration Jefferson AR USA
National Institute of Metrology Beijing China
Q2 Solutions EA Genomics Morrisville NC USA
Sentieon Inc Mountain View CA USA
Seven Bridges Genomics Inc Cambridge MA USA
The Center for Devices and Radiological Health US Food and Drug Administration Silver Spring MD USA
The Center for Drug Evaluation and Research US Food and Drug Administration Silver Spring MD USA
References provided by Crossref.org
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- $a Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing / $c W. Xiao, L. Ren, Z. Chen, LT. Fang, Y. Zhao, J. Lack, M. Guan, B. Zhu, E. Jaeger, L. Kerrigan, TM. Blomquist, T. Hung, M. Sultan, K. Idler, C. Lu, A. Scherer, R. Kusko, M. Moos, C. Xiao, ST. Sherry, OD. Abaan, W. Chen, X. Chen, J. Nordlund, U. Liljedahl, R. Maestro, M. Polano, J. Drabek, P. Vojta, S. Kõks, E. Reimann, BS. Madala, T. Mercer, C. Miller, H. Jacob, T. Truong, A. Moshrefi, A. Natarajan, A. Granat, GP. Schroth, R. Kalamegham, E. Peters, V. Petitjean, A. Walton, TW. Shen, K. Talsania, CJ. Vera, K. Langenbach, M. de Mars, JA. Hipp, JC. Willey, J. Wang, J. Shetty, Y. Kriga, A. Raziuddin, B. Tran, Y. Zheng, Y. Yu, M. Cam, P. Jailwala, C. Nguyen, D. Meerzaman, Q. Chen, C. Yan, B. Ernest, U. Mehra, RV. Jensen, W. Jones, JL. Li, BN. Papas, M. Pirooznia, YC. Chen, F. Seifuddin, Z. Li, X. Liu, W. Resch, J. Wang, L. Wu, G. Yavas, C. Miles, B. Ning, W. Tong, CE. Mason, E. Donaldson, S. Lababidi, LM. Staudt, Z. Tezak, H. Hong, C. Wang, L. Shi
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