Increasing power of genome-wide association studies by collecting additional single-nucleotide polymorphisms

Genetics

Volumn 188, Issue 2, 2011, Pages 449-460

  Kostem, Emrah ^a   Lozano, Jose A ^c   Eskin, Eleazar ^a,b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CASE CONTROL STUDY; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; FOLLOW UP; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE MAP; HUMAN; HUMAN GENETICS; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

ALGORITHMS; ARTHRITIS, RHEUMATOID; CORONARY ARTERY DISEASE; CROHN DISEASE; DIABETES MELLITUS, TYPE 1; DIABETES MELLITUS, TYPE 2; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 79958206616     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.111.128595     Document Type: Article

References (18)

1. Altshuler, D., L. D. Brooks, A. Chakravarti, F. S. Collins, M. J. Daly et al., 2005 A haplotype map of the human genome. Nature 437: 1299-1320.
2. Carlson, C. S., M. A. Eberle, M. J. Rieder, Q. Yi, L. Kruglyak et al., 2004 Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74: 106-120.
3. Cousin, E., E. Genin, S. Mace, S. Ricard, C. Chansac et al., 2003 Association studies in candidate genes: strategies to select SNPs to be tested. Hum. Hered. 56: 151-159.
4. Cousin, E., J. F. Deleuze and E. Genin, 2006 Selection of SNP subsets for association studies in candidate genes: comparison of the power of different strategies to detect single disease susceptibility locus effects. BMC Genet. 7: 20.
5. de Bakker, P. I. W., R. Yelensky, I. Pe'er, S. B. Gabriel, M. J. Daly et al., 2005 Efficiency and power in genetic association studies. Nat. Genet. 37: 1217-1223.
6. Halperin, E., G. Kimmel and R. Shamir, 2005 Tag SNP selection in genotype data for maximizing SNP prediction accuracy. Bioinformatics 21(Suppl. 1): i195-i203.
7. Han, B., H. M. Kang and E. Eskin, 2009 Rapid and accurate multiple testing correction and power estimation for millions of correlated markers. PLoS Genet. 5: e1000456.
8. Hindorff, L. A., P. Sethupathy, H. A. Junkins, E. M. Ramos, J. P. Mehta et al., 2009 Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106: 9362-9367.
9. Lin, Z., and R. B. Altman, 2004 Finding haplotype tagging SNPs by use of principal components analysis. Am. J. Hum. Genet. 75: 850-861.
10. 1000 Genomes Project Consortium, 2010 A map of human genome variation from population-scale sequencing. Nature 467: 1061.
11. Pardi, F., C. M. Lewis and J. C. Whittaker, 2005 SNP selection for association studies: maximizing power across SNP choice and study size. Ann. Hum. Genet. 69: 733-746.
12. Pritchard, J. K., and M. Przeworski, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
13. Qin, Z. S., S. Gopalakrishnan and G. R. Abecasis, 2006 An efficient comprehensive search algorithm for tag SNP selection using linkage disequilibrium criteria. Bioinformatics 22: 220-225.
14. Saccone, S. F., J. P. Rice and N. L. Saccone, 2006 Power-based, phase-informed selection of single nucleotide polymorphisms for disease association screens. Genet. Epidemiol. 30: 459-470.
15. Santana, R., A. Mendiburu, N. Zaitlen, E. Eskin and J. A. Lozano, 2010 Multi-marker tagging single nucleotide polymorphism selection using estimation of distribution algorithms. Artif. Intell. Med. 50: 193-201.
16. Stram, D. O., 2004 Tag SNP selection for association studies. Genet. Epidemiol. 27: 365-374.
17. Stram, D. O., 2005 Software for tag single nucleotide polymorphism selection. Hum. Genomics 2: 144-151.
18. 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.