Testing Gene-Gene Interactions in Genome Wide Association Studies

Genetic Epidemiology

Volumn 38, Issue 2, 2014, Pages 123-134

  Hu, Jie Kate ^a   Wang, Xianlong ^b   Wang, Pei ^b,c  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Gene gene interaction; GWAS; Linkage disequilibrium; Logistic regression; Penetrance

Indexed keywords

ARTICLE; AUTOSOMAL DOMINANT DISORDER; AUTOSOMAL RECESSIVE DISORDER; CONTROLLED STUDY; GENE INTERACTION; GENETIC ASSOCIATION; GENETIC MARKER; PRACTICE GUIDELINE; SIMULATION;

GENE-GENE INTERACTION; GWAS; LINKAGE DISEQUILIBRIUM; LOGISTIC REGRESSION; PENETRANCE;

DISEASE; EPISTASIS, GENETIC; GENES, DOMINANT; GENES, RECESSIVE; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; LOGISTIC MODELS; MODELS, GENETIC; PENETRANCE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84892492069     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21786     Document Type: Article

References (42)

1. Bateson W. 1909. Mendel's Principles of Heredity. Cambridge University Press, Cambridge.
2. Chakravarti A. 1999. Population genetics making sense out of sequence. Nat Genet 21(1 Suppl):56-60.
3. 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.
4. Cordell HJ. 2009. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10:392-404.
5. Donnelly P. 2008. Progress and challenges in genome-wide association studies in humans. Nature 456:728-731.
6. Fisher RA. 1918. The correlation between relatives on the supposition of Mendelian inheritance. Trans R Soc Edin 52:399-433.
7. Goldstein DB. 2009. Common genetic variation and human traits. N Engl J Med 360:1696-1698.
8. Hardy J, Singleton A. 2009. Genomewide association studies and human disease. N Engl J Med 360:1759-1768.
9. Hirschhorn JN. 2009. Genomewide association studies illuminating biologic pathways. N Engl J Med 360:1699-1701.
10. Hirschhorn JN, Daly MJ. 2005. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95-108.
11. Kajiwara K, Berson EL, Dryja TP. 1994. Digenic retinitis pigmentosa due to mutations at the unlinked peripherin/RDS and ROM1 loci. Science 264:1604-1608.
12. Kam-Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, Erhardt-Lehmann A, Hemmer B, Rieckmann P, Daake M, Weber F and others. 2011. EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units. Eur J Hum Genet 19:465-471.
13. Kooperberg C, Leblanc M, Dai JY, Rajapakse I. 2009. Structures and assumptions: strategies to harness gene x gene and gene x environment interactions in GWAS. Stat Sci 24:472-488.
14. Kraft P, Cox DG. 2008. Study designs for genome-wide association studies. Adv Genet 60:465-504.
15. Kraft P, Hunter DJ. 2009. Genetic risk prediction are we there yet? N Engl J Med 360:1701-1703.
16. Ku CS, Loy EY, Pawitan Y, Chia KS. 2010. The pursuit of genome-wide association studies: where are we now? J Hum Genet 55:195-206.
17. Kullback S. 1967. On testing correlation matrices. J R Stat Soc Series C 16:80-85.
18. Larntz K, Perlman MD. 1988. A Simple Test for the Equality of Correlation Matrices IV, vol. 2, Springer-Verlag, New York:289-298.
19. Levy-Lahad E, Lahad A, Eisenberg S, Dagan E, Paperna T, Kasinetz L, Catane R, Kaufman B, Beller U, Renbaum P and others. 2001. A single nucleotide polymorphism in the RAD51 gene modifies cancer risk in BRCA2 but not BRCA1 carriers. Proc Natl Acad Sci USA 98:3232-3236.
20. Liu D, Ghosh D, Lin X. 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics 9:292.
21. Manolio TA, Brooks LD, Collins FS. 2008. A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118:1590-1605.
22. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A and others. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
23. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9:356-369.
24. Moore JH, Asselbergs FW, Williams SM. 2010. Bioinformatics challenges for genome-wide association studies. Bioinformatics 26:445-455.
25. Moore JH, Williams SM. 2005. Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. BioEssays 27:637-646.
26. Moore JH, Williams SM. 2009. Epistasis and its implications for personal genetics. Am J Hum Genet 85:309-320.
27. Neuman RJ, Rice JP, Chakravarti A. 1992. Two-locus models of disease. Genet Epidemiol 9:347-365.
28. Reich DE, Lander ES. 2001. On the allelic spectrum of human disease. Trends Genet 17:502-510.
29. Risch N. 1990. Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet 46:222-228.
30. Seng KC, Seng CK. 2008. The success of the genome-wide association approach: a brief story of a long struggle. Eur J Hum Genet 16:554-564.
31. Teo YY. 2008. Common statistical issues in genome-wide association studies: a review on power, data quality control, genotype calling and population structure. Curr Opin Lipidol 19:133-143.
32. Ueki M, Cordel HJ. 2012. Improved statistics for genome-wide interaction analysis. PLoS Genet 8:e1002625.
33. Wang WY, Barratt BJ, Clayton DG, Todd JA. 2005. Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6:109-118.
34. Weir B. 1996. Genetic Data Analysis II., vol. II. Sinauer Associates, Massachusetts.
35. Wellek S, Ziegler A. 2008. A genotype-based approach to assessing the association between single nucleotide polymorphisms. Hum Hered 67:128-139.
36. Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X. 2010. Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet 86:929-942.
37. Wu X, Jin L, Xiong M. 2008. Composite measure of linkage disequilibrium for testing interaction between unlinked loci. Eur J Hum Genet 16:644-651.
38. Yang Q, Khoury MJ, Sun F, Flanders WD. 1999. Case-only design to measure gene-gene interaction. Epidemiology 10:167-170.
39. Yang Y, He C, Ott J. 2009a. Testing association with interactions by partitioning chi-squares. Ann Hum Genet 73:109-117.
40. Yang C, He Z, Wan X, Yang Q, Xue H, Yu W. 2009b. SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. Bioinformatics 25:504-511.
41. Zhao J, Jin L, Xiong M. 2006. Test for interaction between two unlinked loci. Am J Hum Genet 79:831-845.
42. Ziegler A, König IR, Thompson JR. 2008. Biostatistical aspects of genome-wide association studies. Biom J 50:8-28.