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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Abstract

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.

Type Journal
ISBN 1546-1696 (Electronic) 1087-0156 (Linking)
Authors Xiao, W.; Ren, L.; Chen, Z.; Fang, L. T.; Zhao, Y.; Lack, J.; Guan, M.; Zhu, B.; Jaeger, E.; Kerrigan, L.; Blomquist, T. M.; Hung, T.; Sultan, M.; Idler, K.; Lu, C.; Scherer, A.; Kusko, R.; Moos, M.; Xiao, C.; Sherry, S. T.; Abaan, O. D.; Chen, W.; Chen, X.; Nordlund, J.; Liljedahl, U.; Maestro, R.; Polano, M.; Drabek, J.; Vojta, P.; Koks, S.; Reimann, E.; Madala, B. S.; Mercer, T.; Miller, C.; Jacob, H.; Truong, T.; Moshrefi, A.; Natarajan, A.; Granat, A.; Schroth, G. P.; Kalamegham, R.; Peters, E.; Petitjean, V.; Walton, A.; Shen, T. W.; Talsania, K.; Vera, C. J.; Langenbach, K.; de Mars, M.; Hipp, J. A.; Willey, J. C.; Wang, J.; Shetty, J.; Kriga, Y.; Raziuddin, A.; Tran, B.; Zheng, Y.; Yu, Y.; Cam, M.; Jailwala, P.; Nguyen, C.; Meerzaman, D.; Chen, Q.; Yan, C.; Ernest, B.; Mehra, U.; Jensen, R. V.; Jones, W.; Li, J. L.; Papas, B. N.; Pirooznia, M.; Chen, Y. C.; Seifuddin, F.; Li, Z.; Liu, X.; Resch, W.; Wang, J.; Wu, L.; Yavas, G.; Miles, C.; Ning, B.; Tong, W.; Mason, C. E.; Donaldson, E.; Lababidi, S.; Staudt, L. M.; Tezak, Z.; Hong, H.; Wang, C.; Shi, L.
Responsible Garvan Author Dr Timothy Mercer
Publisher Name NATURE BIOTECHNOLOGY
Published Date 2021-09-30
Published Volume 39
Published Issue 9
Published Pages 1141-1150
Status Published in-print
DOI 10.1038/s41587-021-00994-5
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/34504346