An evaluation of different target enrichment methods in pooled sequencing designs for complex disease association studies

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Day Williams, Aaron G ^a   McLay, Kirsten ^a,b   Drury, Eleanor ^a   Edkins, Sarah ^a   Coffey, Alison J ^a   Palotie, Aarno ^a,c,d   Zeggini, Eleftheria ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b EARLHAM INSTITUTE   (United Kingdom)

^c UNIVERSITY OF HELSINKI   (Finland)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTIC METHOD; ARTICLE; CALCULATION; CONTROLLED STUDY; GENE FREQUENCY; GENETIC ASSOCIATION; INTERMETHOD COMPARISON; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE ENRICHMENT METHOD;

BIOLOGICAL MARKERS; DNA; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84858188091     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026279     Document Type: Article

References (26)

1. Eichler E, Flint J, Gibson G, Kong A, Leal S, et al. (2010) Missing heritability and strategies for _nding the underlying causes of complex disease. Nat Rev Genet 11: 446-450.
2. Manolio T, Collins F, Cox N, Goldstein D, Hindorff L, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
3. Johansen C, Wang J, Lanktree M, Cao H, McIntyre A, et al. (2010) Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. Nat Genet 42: 684-687.
4. Durbin R, Abecasis G, Altshuler D, Auton A, Brooks L, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
5. Nejentsev S, Walker N, Riches D, Egholm M, JA T, (2009) Rare variants of ifih1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324: 387-389.
6. V B (2010) A statistical method for the detection of variants from next-generation resequencing of dna pools. Bioinformatics 26: i318-324.
7. Calvo S, Tucker E, Compton A, Kirby D, Crawford G, et al. (2010) High-throughput, pooled sequencing identifies mutations in nubpl and foxred1 in human complex i deficiency. Nat Genet 42: 851-858.
8. Druley T, Vallania F, Wegner D, Varley K, Knowles O, et al. (2009) Quantification of rare allelic variants from pooled genomic dna. Nat Methods 6: 263-265.
9. Ingman M, Gyllensten U, (2009) Snp frequency estimation using massively parallel sequencing of pooled dna. Eur J Hum Genet 17: 383-386.
10. Koboldt D, Chen K, Wylie T, Larson D, McLellan M, et al. (2009) Varscan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283-2285.
11. Out A, van Minderhout I, Goeman J, Ariyurek Y, Ossowski S, et al. (2009) Deep sequencing to reveal new variants in pooled dna samples. Hum Mutat 30: 1703-1712.
12. Vallania F, Druley T, Ramos E, Wang J, Borecki I, et al. (2010) High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res 20: 1711-1718.
13. Albert T, Molla M, Muzny D, Nazareth L, Wheeler D, et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4: 903-905.
14. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust E, et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27: 182-189.
15. Okou D, Steinberg K, Middle C, Cutler D, Albert T, et al. (2007) Microarray-based genomic selection for high-throughput resequencing. Nat Methods 4: 907-909.
16. Tewhey R, Nakano M, Wang X, Pabon-Pena C, Novak B, et al. (2009) Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol 10: R116.
17. Mamanova L, Coffey A, Scott C, Kozarewa I, Turner E, et al. (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7: 111-118.
18. Teer J, Bonnycastle L, Chines P, Hansen N, Aoyama N, et al. (2010) Systematic comparison of three genomic enrichment methods for massively parallel dna sequencing. Genome Res 20: 1420-1431.
19. Lawrence R, Day-Williams A, Elliott K, Morris A, E Z, (2010) CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies. BMC Bioinformatics 11: 527.
20. Li H, Ruan J, Durbin R, (2008) Mapping short dna sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
21. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: A mapreduce framework for analyzing next-generation dna sequencing data. Genome Res 20: 1297-1303.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and samtools. Bioinformatics 25: 2078-2079.
23. Smit A, Hubley R, Green P, (1996-2010) Repeatmasker open-3.0. URLhttp://www.repeatmasker.org.
24. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
25. Pruitt K, Harrow J, Harte R, Wallin C, Diekhans M, et al. (2009) The consensus coding sequence (ccds) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 19: 1316-1323.
26. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URLhttp://www.R-project.org. ISBN 3-900051-07-0.