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Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9846-51. doi: 10.1073/pnas.1607794113. Epub 2016 Aug 15.

Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing.

Author information

1
Ludwig Center for Cancer Genetics and Therapeutics, Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21287; The Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21231;
2
Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21205; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205;
3
Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794;
4
Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794; Department of Medicine, Stony Brook University, Stony Brook, NY 11794;
5
Ludwig Center for Cancer Genetics and Therapeutics, Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21287; bertvog@gmail.com kinzlke@jhmi.edu.
6
Ludwig Center for Cancer Genetics and Therapeutics, Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21287; The Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21231; Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231 bertvog@gmail.com kinzlke@jhmi.edu.
7
Ludwig Center for Cancer Genetics and Therapeutics, Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21287; Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231.

Abstract

We present the bottleneck sequencing system (BotSeqS), a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. We use BotSeqS to show age- and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal human tissues can vary by several orders of magnitude, depending on biologic and environmental factors. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues.

KEYWORDS:

aging; genomics; next-generation sequencing; somatic mutation

PMID:
27528664
PMCID:
PMC5024639
DOI:
10.1073/pnas.1607794113
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

B.V. has no conflict of interest with respect to the new technology described in this manuscript, as defined by Johns Hopkins University's policy on conflict of interest. B.V. is a founder of PapGene and Personal Genome Diagnostics and a member of the Scientific Advisory Boards of Morphotek and Syxmex-Inostics. These companies and others have licensed patent applications on genetic technologies from Johns Hopkins, some of which result in royalty payments to B.V. The terms of these arrangements are being managed by Johns Hopkins University in accordance with its conflict of interest policies.

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