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


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
doi: 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:

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


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