Using functional annotation for the Empirical determination of Bayes factors for genome-wide association study analysis

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Knight, Jo ^a,b   Barnes, Michael R ^a,c   Breen, Gerome ^a   Weale, Michael E ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b and University of Bristol   (United Kingdom)

^c GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CALCULATION; CHROMATIN; CONTROLLED STUDY; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC DATABASE; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; HUMAN;

BAYES THEOREM; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; QUANTITATIVE TRAIT LOCI;

EID: 79955683639     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014808     Document Type: Article

References (25)

1. Barrett JC, Lee JC, Lees CW, Prescott NJ, Anderson CA, et al. (2009) Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat Genet 15: 15.
2. Welcome 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.
3. Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, et al. (2007) A whole-genome association study of major determinants for host control of HIV-1. Science 317: 944-947.
4. Raychaudhuri S, Plenge RM, Rossin EJ, Ng AC, Purcell SM, et al. (2009) Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet 5: e1000534.
5. Soranzo N, Rivadeneira F, Chinappen-Horsley U, Malkina I, Richards JB, et al. (2009) Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. PLoS Genet 5: e1000445.
6. Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 10: 10.
7. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
8. Lee PH, Shatkay H, (2009) An integrative scoring system for ranking SNPs by their potential deleterious effects. Bioinformatics 25: 1048-1055.
9. Karchin R, (2009) Next generation tools for the annotation of human SNPs. Brief Bioinform 10: 35-52.
10. Genovese CR, Roeder K, Wasserman L, (2006) False discovery control with p-value weighting. Biometrika 93: 509-524.
11. Li C, Li M, Lange EM, Watanabe RM, (2008) Prioritized subset analysis: improving power in genome-wide association studies. Hum Hered 65: 129-141.
12. Roeder K, Bacanu SA, Wasserman L, Devlin B, (2006) Using linkage genome scans to improve power of association in genome scans. Am J Hum Genet 78: 243-252.
13. Saccone SF, Saccone NL, Swan GE, Madden PA, Goate AM, et al. (2008) Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics 24: 1805-1811.
14. Sun L, Craiu RV, Paterson AD, Bull SB, (2006) Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet Epidemiol 30: 519-530.
15. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA, A Catalog of Published Genome-Wide Association Studies. Available at: www.genome.gov/gwastudies. Accessed 2010 May 21.
16. Johnson AD, O'Donnell CJ, (2009) An open access database of genome-wide association results. BMC Med Genet 10: 6.
17. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888.
18. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, et al. (2007) A genome-wide association study of global gene expression. Nat Genet 39: 1202-1207.
19. Davuluri RV, Grosse I, Zhang MQ, (2001) Computational identification of promoters and first exons in the human genome. Nat Genet 29: 412-417.
20. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, et al. (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24: 2938-2939.
21. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
22. Stephens M, Balding DJ, (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10: 681-690.
23. Wakefield J, (2009) Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol 33: 79-86.
24. Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet.
25. Bentley DR, (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16: 545-552.