Variant discovery in targeted resequencing using whole genome amplified DNA

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Indap, Amit R ^a   Cole, Regina ^b   Runge, Christina L ^b   Marth, Gabor T ^a   Olivier, Michael ^c  

^a BOSTON COLLEGE   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

^c SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Capture sequencing; Next generation sequencing; Variant discovery; Whole genome amplified DNA

Indexed keywords

DNA; GENOMIC DNA; UNCLASSIFIED DRUG; WHOLE GENOME AMPLIFIED DNA;

ALLELE; ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; GENE AMPLIFICATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; INDEL MUTATION; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME AMPLIFICATION;

ALLELES; COMPUTER GRAPHICS; DNA; GENETIC VARIATION; GENOMICS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEQUENCE ANALYSIS, DNA;

EID: 84880024289     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-468     Document Type: Article

References (28)

1. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature 2009, 461(7265):747-753. 10.1038/nature08494, 2831613, 19812666.
2. Maher B. Personal genomes: the case of the missing heritability. Nature 2008, 456(7218):18-21. 10.1038/456018a, 18987709.
3. Bentley DR, Balasubramanian, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517, 2581791,2581791, 18987734.
4. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Lisa A, Berka J, Braverman MS, Chen Y, Gomes XV, Goodwin BC, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Chen Z Genome sequencing in open microfabricated high density picoliter reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220, Chen Z.
5. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-1073. 10.1038/nature09534, 3042601, 20981092.
6. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR. Genome-wide in situ exon capture for selective resequencing. Nat Genet 2007, 39(12):1522-1527. 10.1038/ng.2007.42, 17982454.
7. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27(2):182-189. 10.1038/nbt.1523, 2663421, 19182786.
8. Shendure J. Next-generation human genetics. Genome Biol 2011, 12(9):408. 10.1186/gb-2011-12-9-408, 3308046, 21920048.
9. Clark MJ, Chen R, Lam HYK, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 2011, 29(10):908-914. 10.1038/nbt.1975, 21947028.
10. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. Exome sequencing identifies the cause of a Mendelian disorder. Nat Genet 2010, 42:30-35. 10.1038/ng.499, 2847889, 19915526.
11. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 2011, 12(11):745-755. 10.1038/nrg3031, 21946919.
12. Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, Depristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs RA. The functional spectrum of low-frequency coding variation. Genome Biol 2011, 12(9):R84. 10.1186/gb-2011-12-9-r84, 3308047, 21917140.
13. Lasken RS, Egholm M. Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends in Biotechnol 2003, 21(12):531-535.
14. Xing J, Watkins WS, Zhang Y, Witherspoon DJ, Jorde LB. High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays. Genomics 2008, 92(6):452-456. 10.1016/j.ygeno.2008.08.007, 2659594, 18786630.
15. Berthier-Schaad Y, Kao WH, Coresh J, Zhang L, Ingersoll RG, Stephens R, Smith MW. Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies. Electrophoresis 2007, 28(16):2812-2817. 10.1002/elps.200600674, 17702060.
16. He YJ, Misher AD, Irvin W, Motsinger-Reif A, McLeod HL, Hoskins JM. Assessing the utility of whole genome amplified DNA as a template for DMET Plus array. Clin Chem Lab Med 2012, 50(8):1329-1334.
17. Murphy SJ, Cheville JC, Zarei S, Johnson SH, Sikkink RA, Kosari F, Feldman AL, Eckloff BW, Karnes RJ, Vasmatzis G. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer. DNA Res 2012, 19(5):395-406. 10.1093/dnares/dss021, 3473372, 22991452.
18. Jiang T, Yang L, Jiang H, Tian G, Zhang X. High-performance single-chip exon capture allows accurate whole exome sequencing using the Illumina Genome Analyzer. Sci China Life Sci 2011, 54(10):945-952. 10.1007/s11427-011-4232-4, 22038007.
19. ElSharawy A, Warner J, Olson J, Forster M, Schilhabel MB, Link DR, Rose-John S, Schreiber S, Rosenstiel P, Brayer J, Franke A. Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing. BMC Genomics 2012, 13:500. 10.1186/1471-2164-13-500, 3534403, 22994565.
20. Picard homepage. [http://picard.sourceforge.net].
21. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36:e105. 10.1093/nar/gkn425, 2532726, 18660515.
22. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis A, Del Angel G, Rivas M, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011,
23. Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, Sunyaev SR. Exome sequencing and the genetic basis of complex traits. Nat Genet 2012, 44(6):623-630. 10.1038/ng.2303, 22641211.
24. Kissebah AH, Sonnenberg GE, Myklebust J, Goldstein M, Broman K, James RG, Marks JA, Krakower GR, Jacob HJ, Weber J, Martin L, Blangero J, Comuzzie AG. Quantitative trait loci on chromosomes 3 and 17 influence phenotypes of the Metabolic Syndrome. Proc Natl Acad Sci U S A 2000, 97(26):14478-14483. 10.1073/pnas.97.26.14478, 18944, 11121050.
25. MOSAIK homepage [http://bioinformatics.bc.edu/marthlab/Mosaik], MOSAIK homepage.
26. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
27. R Development Core Team R: A Language and Environment for Statistical Computing 2011, Vienna: R Foundation for Statistical Computing, [http://www.R-project.org/]. [ISBN 3-900051-07-0], R Development Core Team.
28. CRAN Package fmsb. [http://cran.r-project.org/web/packages/fmsb/index.html].