Fast Association Tests for Genes with FAST

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Chanda, Pritam ^a,b   Huang, Hailiang ^c,d   Arking, Dan E ^b   Bader, Joel S ^a,b  

^a JOHNS HOPKINS UNIVERSITY   (United States)

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

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FAST ASSOCIATION TEST; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC PROCEDURES; GENETIC SCREENING; INFORMATION PROCESSING; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; UNIVARIATE ANALYSIS;

COMPUTER SIMULATION; DATABASES, GENETIC; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84880731909     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068585     Document Type: Article

References (22)

1. Consortium WTCC (2007) Genome-wide association study of 14,000 cases of seven common dis-eases and 3,000 shared controls. Nature 447: 661-678.
2. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. (2008) Genome-wide as-sociation studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369.
3. Consortium GP, Durbin RM, Abecasis GR, Altshuler DL, Auton A, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
4. Consortium IH, (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
5. Consortium IH, (2007) A second generation human haplotype map of over 3.1 million snps. Nature 449: 851-861.
6. Li Y, Willer C, Sanna S, Abecasis G, (2009) Genotype imputation. Annu Rev Genomics Hum Genet 10: 387-406.
7. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
8. Aulchenko YS, Struchalin MV, van Duijn CM, (2010) Probabel package for genome-wide association analysis of imputed data. BMC Bioinformatics 11: 134.
9. Huang H, Chanda P, Alonso A, Bader JS, Arking DE, (2011) Gene-based tests of association. PLoS Genet 7: e1002177.
10. Ortega JM, Rheinboldt WC, (2000) Iterative Solution of Nonlinear Equations in Several Variables. Classics in Applied Mathematics. SIAM.
11. Servin B, Stephens M, (2007) Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3: e114.
12. Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, et al. (2010) A versatile gene-based test for genome-wide association studies. Am J Hum Genet 87: 139-145.
13. Li MX, Gui HS, Kwan JSH, Sham PC, (2011) Gates: a rapid and powerful gene-based association test using extended simes procedure. Am J Hum Genet 88: 283-293.
14. Simes RJ, (1986) An improved bonferroni procedure for multiple tests of significance. Biometrika 73: 751-754.
15. Knuth DE (1997) The art of computer programming. Addison-Wesley, 3rd edition, 97002147.
16. Manolio TA, Brooks LD, Collins FS, (2008) A hapmap harvest of insights into the genetics of common disease. J Clin Invest 118: 1590-1605.
17. 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.
18. Scott RA, Lagou V, Welch RP, Wheeler E, Montasser ME, et al. (2012) Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying bio-logical pathways. Nat Genet 44: 991-1005.
19. Cornelis MC, Monda KL, Yu K, Paynter N, Azzato EM, et al. (2011) Genome-wide meta-analysis identifies regions on 7p21 (ahr) and 15q24 (cyp1a2) as determinants of habitual caffeine consump-tion. PLoS Genet 7: e1002033.
20. Camargo M, Rivera D, Moreno L, Lidral AC, Harper U, et al. (2012) Gwas reveals new recessive loci associated with non-syndromic facial clefting. Eur J Med Genet 55: 510-514.
21. Tang CS, Ferreira MAR, (2012) A gene-based test of association using canonical correlation analysis. Bioinformatics 28: 845-850.
22. Bacanu SA, (2012) On optimal gene-based analysis of genome scans. Genet Epidemiol 36: 333-339.