11/19/2023 0 Comments False negative![]() Mutation calls from two cell-line databases including GDSC (Genomics of Drug Sensitivity in Cancer) and CCLE (Cancer Cell Line Encyclopedia) were constructed by whole-exome- or equivalently highly-multiplex NGS inconsistent mutation calls have been reported to be as high as 43%, suggesting a possible high rate of error in NGS. To establish any firm regulatory rules, further studies on the reproducibility or reliability of NGS results are needed.įor NGS analyses, target enrichment, amplification, sequencing processes, and bioinformatics analyses are involved, but the estimation of NGS errors have not been comprehensive. The Food and Drug Administration (FDA) has finalized a guidance document to accelerate the establishment of a regulatory approach for NGS testing, though the actual regulations are still debated. Currently, in the USA, the clinical laboratories for NGS testing are overseen by the Centers for Medicare and Medicaid Services (CMS) according to the Clinical Laboratory Improvement Amendments (CLIA) regulations. Some of the errors seem to be related to the NGS instrumentation itself, the SOLiD platform having shown an erroneous variant calling rate as high as 20–40% in a study. In a study with 20,000 samples, the NGS false-positive rate was 1.3%, the authors suggesting that Sanger confirmation is required for NGS panel testing. ![]() Despite widespread adoption of NGS technology for the purposes of clinical diagnosis, high error rates on various NGS platforms has been reported (0.26–12.86%). According to the American Clinical Laboratory Association (ACLA), over 11,000 laboratories and companies in the USA have developed their own NGS tests. Whereas classical genetic tests measure limited base changes or structural changes in DNA, recently introduced next-generation sequencing (NGS) technology can examine millions of DNA variants at a time. Whole-exome-next-generation sequencing TP, H.Ĭompeting interests: The authors have declared that no competing interests exist. All other data are available in supplementary tables.įunding: This study was supported by grants from the National Cancer Center (NCC), Korea (1510121, 1831130, 1811030, and 1910150), and a grant from the National Research Foundation, Korea (NRF-2015R1A2A2A04007432) to K-M. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: MAF files from our targeted NGS in 35 cell lines are available at as described in Materials and Methods. ![]() Received: JAccepted: AugPublished: September 12, 2019Ĭopyright: © 2019 Kim et al. PLoS ONE 14(9):Įditor: Amanda Ewart Toland, Ohio State University Wexner Medical Center, UNITED STATES (2019) False-negative errors in next-generation sequencing contribute substantially to inconsistency of mutation databases. Citation: Kim Y-H, Song Y, Kim J-K, Kim T-M, Sim HW, Kim H-L, et al. ![]()
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