Introduction to genetic association studies

Cold Spring Harbor Protocols

Volumn 7, Issue 3, 2012, Pages 297-306

  Lewis, Cathryn M ^a   Knight, Jo ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CASE CONTROL STUDY; DISEASE ASSOCIATION; GENE IDENTIFICATION; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC MARKER; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; QUANTITATIVE TRAIT LOCUS; RISK ASSESSMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; GENETIC PREDISPOSITION; METHODOLOGY; REVIEW;

CASE-CONTROL STUDIES; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS;

EID: 84857831217     PISSN: 19403402     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top068163     Document Type: Article

References (27)

1. Altshuler D, Hirschhorn JN, Klannemark M, Lindgren CM, Vohl MC, Nemesh J, Lane CR, Schaffner SF, Bolk S, Brewer C, et al. 2000. The common PPARg Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat Genet 26: 76-80.
2. Antoniou AC, Easton DF. 2003. Polygenic inheritance of breast cancer: Implications for design of association studies. Genet Epidemiol 25: 190-202.
3. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, et al. 2005. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37: 1243-1246.
4. Cordell HJ. 2002. Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11: 2463-2468.
5. Cordell HJ, Clayton DG. 2002. A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: Application to HLA in type 1 diabetes. Am J Hum Genet 70: 124-141.
6. de Bakker PI, Yelensky R, Péer I, Gabriel SB, Daly MJ, Altshuler D. 2005. Efficiency and power in genetic association studies. Nat Genet 37: 1217-1223.
7. Devlin B, Risch N. 1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29: 311-322.
8. Devlin B, Roeder K. 1999. Genomic control for association studies. Biometrics 55: 997-1004.
9. Devlin B, Bacanu SA, Roeder K. 2004. Genomic control to the extreme. Nat Genet 36: 1129-1130; author reply 1131.
10. Excoffier L, Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
11. Ioannidis JP, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. 2001. Replication validity of genetic association studies. Nat Genet29:306-309.
12. Ioannidis JP, Ntzani EE, Trikalinos TA. 2004. "Racial" differences in genetic effects for complex diseases. Nat Genet 36: 1312-1318.
13. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN. 2003. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet 33: 177-182.
14. Marchini J, Donnelly P, Cardon LR. 2005. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37: 413-417.
15. Mathew CG, Lewis CM. 2004. Genetics of inflammatory bowel disease: Progress and prospects. Hum Mol Genet 13: R161-R168.
16. Milne RL, Fagerholm R, Nevanlinna H, Benitez J. 2008. The importance of replication in gene-gene interaction studies: Multifactor dimensionality reduction applied to a two-stage breast cancer case-control study. Car-cinogenesis 29: 1215-1218.
17. O'Donovan MC, Craddock N, Norton N, Williams H, Peirce T, Moskvina V, Nikolov I, Hamshere M, Carroll L, Georgieva L, et al. 2008. Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet 40: 1050-1055.
18. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
19. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
20. Purcell S, Cherny SS, Sham PC. 2003. Genetic Power Calculator: Design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19: 149-150.
21. Ritchie MD, Hahn LW, Moore JH. 2003. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemiol 24: 150-157.
22. Sasieni PD. 1997. From genotypes to genes: Doubling the sample size. Biometrics 53: 1253-1261.
23. Sham PC, Rijsdijk FV, Knight J, Makoff A, North B, Curtis D. 2004. Haplo-type association analysis of discrete and continuous traits using mixture of regression models. Behav Genet 34: 207-214.
24. Slatkin M. 1999. Disequilibrium mapping of a quantitative-trait locus in an expanding population. Am J Hum Genet 64: 1764-1772.
25. Spielman RS, McGinnis RE, Ewens WJ. 1993. Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52: 506-516.
26. Steer S, Lad B, Grumley JA, Kingsley GH, Fisher SA. 2005. Association of R602W in a protein tyrosine phosphatase gene with a high risk of rheumatoid arthritis in a British population: Evidence for an early onset/ disease severity effect. Arthritis Rheum 52: 358-360.
27. Wellcome Trust Case Control Consortium (WTCCC). 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.