False-negative errors in next-generation sequencing contribute substantially to inconsistency of mutation databases

English version

Autoři: Young-Ho Kim ^aff001; Yura Song ^aff001; Jong-Kwang Kim ^aff001; Tae-Min Kim ^aff002; Hye Won Sim ^aff001; Hyung-Lae Kim ^aff003; Hyonchol Jang ^aff001; Young-Woo Kim ^aff004; Kyeong-Man Hong ^aff001
Působiště autorů: Research Institute, National Cancer Center, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Korea ^aff001; Department of Medical Informatics and Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea ^aff002; Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Korea ^aff003; Center for Gastric Cancer, National Cancer Center Hospital, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Korea ^aff004
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0222535

Souhrn

Background

More than 11,000 laboratories and companies developed their own next-generation sequencing (NGS) for screening and diagnosis of various diseases including cancer. Although inconsistencies of mutation calls as high as 43% in databases such as GDSC (Genomics of Drug Sensitivity in Cancer) and CCLE (Cancer Cell Line Encyclopedia) have been reported, not many studies on the reasons for the inconsistencies have been published. Methods: Targeted-NGS analysis of 151 genes in 35 cell lines common to GDSC and CCLE was performed, and the results were compared with those from GDSC and CCLE wherein whole-exome- or highly-multiplex NGS were employed.

Results

In the comparison, GDSC and CCLE had a high rate (40–45%) of false-negative (FN) errors which would lead to high rate of inconsistent mutation calls, suggesting that highly-multiplex NGS may have high rate of FN errors. We also posited the possibility that targeted NGS, especially for the detection of low-level cancer cells in cancer tissues might suffer significant FN errors.

Conclusion

FN errors may be the most important errors in NGS testing for cancer; their evaluation in laboratory-developed NGS tests is needed.

Klíčová slova:

Biology and life sciences – Genetics – Genomics – Genome analysis – Computational biology – Research and analysis methods – Molecular biology – Evolutionary biology – Database and informatics methods – Bioinformatics – Sequence analysis – Gene identification and analysis – Molecular biology techniques – Mutation – Evolutionary genetics – Sequence databases – Biological databases – Sequencing techniques – Transcriptome analysis – Genomic databases – Mutation databases – DNA sequencing – Next-generation sequencing – Nonsense mutation – Mutation detection

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