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

Proceedings of the National Academy of Sciences of the United States of America

Volumn 113, Issue 35, 2016, Pages 9846-9851

  Hoang, Margaret L ^a,b,f   Kinde, Isaac ^a,b,g   Tomasetti, Cristian ^a,c   McMahon, K Wyatt ^a,b   Rosenquist, Thomas A ^d   Grollman, Arthur P ^d   Kinzler, Kenneth W ^a   Vogelstein, Bert ^a,b,e   Papadopoulos, Nickolas ^a,e  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^d STONY BROOK UNIVERSITY   (United States)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f NANOSTRING TECHNOLOGIES   (United States)

^g PapGene Inc   (United States)

Author keywords

Aging; Enomics; Next generation sequencing; Somatic mutation

Indexed keywords

CARCINOGEN; CELL NUCLEUS DNA; GENOMIC DNA; MITOCHONDRIAL DNA;

ADULT; AGE; ARTICLE; DILUTION; DNA BARCODING; DNA REPAIR; ENVIRONMENTAL FACTOR; FRONTAL CORTEX; GENE SEQUENCE; GENETIC ANALYZER; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; KIDNEY CORTEX; MIDDLE AGED; MISMATCH REPAIR; MITOCHONDRIAL GENOME; NEXT GENERATION SEQUENCING; NORMAL HUMAN; POINT MUTATION; PRIORITY JOURNAL; SOMATIC MUTATION; ADOLESCENT; AGED; CELL NUCLEUS; CHEMISTRY; CHILD; FEMALE; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; MALE; MUTATION; PRESCHOOL CHILD; PROCEDURES; VERY ELDERLY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; CELL NUCLEUS; CHILD; CHILD, PRESCHOOL; DNA, MITOCHONDRIAL; FEMALE; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MUTATION; YOUNG ADULT;

EID: 84984691299     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1607794113     Document Type: Article

References (36)

1. Stratton MR, Campbell PJ, Futreal PA (2009) The cancer genome. Nature 458(7239): 719-724.
2. Kennedy SR, Loeb LA, Herr AJ (2012) Somatic mutations in aging, cancer and neurodegeneration. Mech Ageing Dev 133(4):118-126.
3. Vijg J (2014) Somatic mutations, genome mosaicism, cancer and aging. Curr Opin Genet Dev 26:141-149.
4. Ross MG, et al. (2013) Characterizing and measuring bias in sequence data. Genome Biol 14(5):R51.
5. Albertini RJ, Nicklas JA, O'Neill JP, Robison SH (1990) In vivo somatic mutations in humans: Measurement and analysis. Annu Rev Genet 24:305-326.
6. Cole J, Skopek TR (1994) International Commission for Protection Against Environmental Mutagens and Carcinogens working paper no. 3: Somatic mutant frequency, mutation rates and mutational spectra in the human population in vivo. Mutat Res 304(1):33-105.
7. Navin N, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472(7341):90-94.
8. Zong C, Lu S, Chapman AR, Xie XS (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338(6114):1622-1626.
9. Wang J, Fan HC, Behr B, Quake SR (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150(2):402-412.
10. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B (2011) Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci USA 108(23):9530-9535.
11. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R (2011) Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci USA 108(50):20166-20171.
12. Schmitt MW, et al. (2012) Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci USA 109(36):14508-14513.
13. Hiatt JB, Pritchard CC, Salipante SJ, O'Roak BJ, Shendure J (2013) Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Res 23(5):843-854.
14. Baslan T, Hicks J (2014) Single cell sequencing approaches for complex biological systems. Curr Opin Genet Dev 26:59-65.
15. Kivioja T, et al. (2011) Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 9(1):72-74.
16. Kinde I, et al. (2013) Evaluation of DNA from the Papanicolaou test to detect ovarian and endometrial cancers. Sci Transl Med 5(167):167ra4.
17. Kumar A, et al. (2014) Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biol 15(12):530.
18. Keys JR, et al. (2015) Primer ID informs next-generation sequencing platforms and reveals preexisting drug resistance mutations in the HIV-1 reverse transcriptase coding domain. AIDS Res Hum Retroviruses 31(6):658-668.
19. Kennedy SR, Salk JJ, Schmitt MW, Loeb LA (2013) Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet 9(9):e1003794.
20. Schmitt MW, et al. (2015) Sequencing small genomic targets with high efficiency and extreme accuracy. Nat Methods 12(5):423-425.
21. Costello M, et al. (2013) Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.
22. Parsons R, et al. (1995) Mismatch repair deficiency in phenotypically normal human cells. Science 268(5211):738-740.
23. Shlien A, et al.; Biallelic Mismatch Repair Deficiency Consortium (2015) Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers. Nat Genet 47(3):257-262.
24. Hoang ML, et al. (2013) Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing. Sci Transl Med 5(197):197ra102.
25. Randerath E, et al. (1989) Covalent DNA damage in tissues of cigarette smokers as determined by 32P-postlabeling assay. J Natl Cancer Inst 81(5):341-347.
26. Ju YS, et al.; ICGC Breast Cancer Group; ICGC Chronic Myeloid Disorders Group; ICGC Prostate Cancer Group (2014) Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 3:3.
27. Kandoth C, et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature 502(7471):333-339.
28. Spalding KL, Bhardwaj RD, Buchholz BA, Druid H, Frisén J (2005) Retrospective birth dating of cells in humans. Cell 122(1):133-143.
29. Lodato MA, et al. (2015) Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350(6256):94-98.
30. Madabhushi R, Pan L, Tsai LH (2014) DNA damage and its links to neurodegeneration. Neuron 83(2):266-282.
31. Kennedy SR, et al. (2014) Detecting ultralow-frequency mutations by duplex sequencing. Nat Protoc 9(11):2586-2606.
32. Scheibye-Knudsen M, Fang EF, Croteau DL, Wilson DM, 3rd, Bohr VA (2015) Protecting the mitochondrial powerhouse. Trends Cell Biol 25(3):158-170.
33. Tomasetti C, Vogelstein B, Parmigiani G (2013) Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proc Natl Acad Sci USA 110(6):1999-2004.
34. Tomasetti C, Vogelstein B (2015) Cancer etiology: Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science 347(6217):78-81.
35. Hamilton SR, et al. (1995) The molecular basis of Turcot's syndrome. N Engl J Med 332(13):839-847.
36. De Vos M, Hayward BE, Picton S, Sheridan E, Bonthron DT (2004) Novel PMS2 pseudogenes can conceal recessive mutations causing a distinctive childhood cancer syndrome. Am J Hum Genet 74(5):954-964.