The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology

Cancer Epidemiology Biomarkers and Prevention

Volumn 24, Issue 8, 2015, Pages 1207-1213

  Zhu, Qianqian ^a   Hu, Qiang ^a   Shepherd, Lori ^a   Wang, Jianmin ^a   Wei, Lei ^a   Morrison, Carl D ^a   Conroy, Jeffrey M ^a   Glenn, Sean T ^a   Davis, Warren ^a   Kwan, Marilyn L ^b   Ergas, Isaac J ^b   Roh, Janise M ^b   Kushi, Lawrence H ^b   Ambrosone, Christine B ^a   Liu, Song ^a   Yao, Song ^a  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

^b DIVISION OF RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA;

ARTICLE; BREAST CANCER; CANCER EPIDEMIOLOGY; CANCER PATIENT; CLINICAL ARTICLE; CODING; COHORT ANALYSIS; DNA EXTRACTION; DNA LIBRARY; DNA MICROARRAY KIT; DNA SEQUENCE; EXOME; FEMALE; GENETIC VARIABILITY; HUMAN; INDEL MUTATION; PRIORITY JOURNAL; PROSPECTIVE STUDY; SALIVA; SEGMENTAL DUPLICATION; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE EXOME SEQUENCING; CONTROLLED STUDY; GENETICS; GENOMICS; NEOPLASMS; PROCEDURES; RANDOMIZED CONTROLLED TRIAL;

DNA; EXOME; GENOMICS; HUMANS; NEOPLASMS; SEQUENCE ANALYSIS, DNA;

EID: 84941789569     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-15-0205     Document Type: Article

References (36)

1. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, et al. The complete genome of an individual bymassively parallelDNAsequencing. Nature 2008;452:872-6.
2. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009;461:272-6.
3. Teer JK, Mullikin JC. Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet 2010;19:R145-51.
4. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al. Exome sequencing identifies the cause of amendelian disorder. Nat Genet 2010;42:30-5.
5. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369:1502-11.
6. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
7. Rabbani B, Tekin M, Mahdieh N. The promise of whole-exome sequencing in medical genetics. J Hum Genet 2014;59:5-15.
8. Johansen Taber KA, Dickinson BD, Wilson M. The promise and challenges of next-generation genome sequencing for clinical care. JAMA Intern Med 2014;174:275-80.
9. Garraway LA. Genomics-driven oncology: framework for an emerging paradigm. J Clin Oncol 2013;31:1806-14.
10. Fitzgerald LM, Kumar A, Boyle EA, Zhang Y, McIntosh LM, Kolb S, et al. Germline missense variants in the BTNL2 gene are associated with prostate cancer susceptibility. Cancer Epidemiol Biomarkers Prev 2013;22:1520-8.
11. Gracia-Aznarez FJ, Fernandez V, Pita G, Peterlongo P, Dominguez O, de la Hoya M, et al. Whole exome sequencing suggests much of non-BRCA1/BRCA2 familial breast cancer is due to moderate and low penetrance susceptibility alleles. PLoS One 2013;8: e55681.
12. Esteban-Jurado C, Vila-Casadesus M, Garre P, Lozano JJ, Pristoupilova A, Beltran S, et al. Whole-exome sequencing identifies rare pathogenic variants in new predisposition genes for familial colorectal cancer. Genet Med 2015;17:131-42.
13. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 2011;29:908-14.
14. Sulonen AM, Ellonen P, Almusa H, Lepisto M, Eldfors S, Hannula S, et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol 2011;12:R94.
15. Asan, Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, et al. Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol 2011;12:R95.
16. Clark MJ, Chen R, Lam HYK, Karczewski KJ, Chen R, Euskirchen G, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotech 2011;29:908-14.
17. Kwan ML, Ambrosone CB, Lee MM, Barlow J, Krathwohl SE, Ergas IJ, et al. The Pathways Study: a prospective study of breast cancer survivorship within Kaiser Permanente Northern California. Cancer Causes Control 2008;19:1065-76.
18. Ambrosone CB, Nesline MK, Davis W. Establishing a cancer center data bank and biorepository for multidisciplinary research. Cancer Epidemiol Biomarkers Prev 2006;15:1575-7.
19. Yan L, Ma C, Wang D, Hu Q, Qin M, Conroy JM, et al. OSAT: a tool for sample-to-batch allocations in genomics experiments. BMC Genomics 2012;13:689.
20. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60.
21. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25: 2078-9.
22. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20:1297-303.
23. Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotech 2014;32:246-51.
24. Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res 2013;41:D936-41.
25. Highnam G, Franck C, Martin A, Stephens C, Puthige A, Mittelman D. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res 2013;41: e32.
26. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, et al. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-73.
27. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, et al. Sequence and structural variation in a human genome uncovered by shortread, massively parallel ligation sequencing using two-base encoding. Genome Res 2009;19:1527-41.
28. Zhang Y, Li B, Li C, Cai Q, Zheng W, Long J. Improved variant calling accuracy by merging replicates in whole-exome sequencing studies. Biomed Res Int 2014;2014:319534.
29. Kidd Jeffrey M, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, et al. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet 2012;91:660-71.
30. The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491: 56-65.
31. Ionita-Laza I, Lange C, M Laird N. Estimating the number of unseen variants in the human genome. Proc Natl Acad Sci U S A 2009;106: 5008-13.
32. Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, et al. The origin, evolution, and functional impact of short insertiondeletion variants identified in 179 human genomes. Genome Res 2013;23:749-61.
33. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res 2015;43:D805-11.
34. Fang H, Wu Y, Narzisi G, O'Rawe JA, Barron LT, Rosenbaum J, et al. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med 2014;6:89.
35. Samarakoon PS, Sorte HS, Kristiansen BE, Skodje T, Sheng Y, Tjonnfjord GE, et al. Identification of copy number variants from exome sequence data. BMC Genomics 2014;15:661.
36. Tan R, Wang Y, Kleinstein SE, Liu Y, Zhu X, Guo H, et al. An evaluation of copy number variation detection tools from whole-exome sequencing data. Hum Mutat 2014;35:899-907.