气候变化领域集成服务门户(CCPortal): Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing

CCPortal

DOI	10.1073/PNAS.2013724117
	Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing
	Valentine C.C.; III; Young R.R.; Fielden M.R.; Kulkarni R.; Williams L.N.; Li T.; Minocherhomji S.; Salk J.J.
发表日期	2021
ISSN	00278424
起始页码	33414
结束页码	33425
卷号	117 期号:52
英文摘要	The ability to accurately measure mutations is critical for basic research and identifying potential drug and chemical carcinogens. Current methods for in vivo quantification of mutagenesis are limited because they rely on transgenic rodent systems that are low-throughput, expensive, prolonged, and do not fully represent other species such as humans. Next-generation sequencing (NGS) is a conceptually attractive alternative for detecting mutations in the DNA of any organism; however, the limit of resolution for standard NGS is poor. Technical error rates (∼1 × 10−3) of NGS obscure the true abundance of somatic mutations, which can exist at per-nucleotide frequencies ≤1 × 10−7. Using duplex sequencing, an extremely accurate error-corrected NGS (ecNGS) technology, we were able to detect mutations induced by three carcinogens in five tissues of two strains of mice within 31 d following exposure. We observed a strong correlation between mutation induction measured by duplex sequencing and the gold-standard transgenic rodent mutation assay. We identified exposure-specific mutation spectra of each compound through trinucleotide patterns of base substitution. We observed variation in mutation susceptibility by genomic region, as well as by DNA strand. We also identified a primordial marker of carcinogenesis in a cancer-predisposed strain of mice, as evidenced by clonal expansions of cells carrying an activated oncogene, less than a month after carcinogen exposure. These findings demonstrate that ecNGS is a powerful method for sensitively detecting and characterizing mutagenesis and the early clonal evolutionary hallmarks of carcinogenesis. Duplex sequencing can be broadly applied to basic mutational research, regulatory safety testing, and emerging clinical applications. © 2020 National Academy of Sciences. All rights reserved.
英文关键词	DNA repair; Error-corrected sequencing; Genetic toxicology; Genotoxicity; Preclinical cancer risk assessment
语种	英语
scopus关键词	carcinogen; trinucleotide; carcinogen; DNA; animal cell; animal experiment; animal model; animal tissue; Article; carcinogenesis; cohort analysis; controlled study; DNA strand; duplex sequencing; gene activation; gene mutation; gene sequence; genetic susceptibility; gold standard; high throughput sequencing; human; in vivo study; male; mouse; mutagenesis; nonhuman; nucleic acid base substitution; oncogene; priority journal; animal; carcinogenesis; cluster analysis; gene locus; genetic transcription; genetics; genome; mutagenesis; mutation; neoplasm; oncogene ras; phenotype; procedures; transgenic mouse; Animals; Carcinogenesis; Carcinogens; Cluster Analysis; DNA; Genes, ras; Genetic Loci; Genome; High-Throughput Nucleotide Sequencing; Humans; Mice, Transgenic; Mutagenesis; Mutation; Neoplasms; Oncogenes; Phenotype; Transcription, Genetic
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/179627
作者单位	TwinStrand Biosciences, Seattle, WA 98121, United States; MilliporeSigma/BioReliance Toxicology Testing Services, Rockville, MD 20850, United States; Amgen Research, Amgen, Thousand Oaks, CA 91320, United States; Expansion Therapeutics, San Diego, CA 92121, United States; EMD Serono Research and Development Institute, Billerica, MA 01821, United States
推荐引用方式 GB/T 7714	Valentine C.C.,III,Young R.R.,et al. Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing[J],2021,117(52).
APA	Valentine C.C..,III.,Young R.R..,Fielden M.R..,Kulkarni R..,...&Salk J.J..(2021).Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing.Proceedings of the National Academy of Sciences of the United States of America,117(52).
MLA	Valentine C.C.,et al."Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing".Proceedings of the National Academy of Sciences of the United States of America 117.52(2021).