A Nonparametric Test to Detect Quantitative Trait Loci Where the Phenotypic Distribution Differs by Genotypes

Genetic Epidemiology

Volumn 37, Issue 4, 2013, Pages 323-333

  Aschard, Hugues ^a   Zaitlen, Noah ^b   Tamimi, Rulla M ^a,c   Lindström, Sara ^a   Kraft, Peter ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Gene gene and gene environment interactions; Genome wide association studies; Nonparametric test; Quantitative trait; Quantitative traits

Indexed keywords

ALLELE; ARTICLE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HEREDITY; HUMAN; LINEAR REGRESSION ANALYSIS; NONPARAMETRIC TEST; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTER SIMULATION; FEMALE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LINEAR MODELS; MAMMOGRAPHY; PHENOTYPE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; SOFTWARE;

EID: 84876413661     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21716     Document Type: Article

References (40)

1. Aschard H, Chen J, Cornelis MC, Chibnik LB, Karlson EW, Kraft P. 2012. Inclusion of gene-gene and gene-environment interactions unlikely to dramatically improve risk prediction for complex diseases. Am J Hum Genet 90(6):962-972.
2. Brittain E. 1987. P-values for the multi-sample Kolmogorov-Smirnov test using the expanded Bonferroni approximation. Commun Stat Theory Methods 16(3):821-835.
3. Byng JW, Boyd NF, Little L, Lockwood G, Fishell E, Jong RA, Yaffe MJ. 1996. Symmetry of projection in the quantitative analysis of mammographic images. Eur J Cancer Prev 5(5):319-327.
4. Churchill GA, Doerge RW. 2008. Naive application of permutation testing leads to inflated type I error rates. Genetics 178(1):609-610.
5. Clayton D, McKeigue PM. 2001. Epidemiological methods for studying genes and environmental factors in complex diseases. Lancet 358(9290):1356-1360.
6. Colditz GA, Hankinson SE. 2005. The Nurses' Health Study: lifestyle and health among women. Nat Rev Cancer 5(5):388-396.
7. Cordell HJ. 2009. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10(6):392-404.
8. Cornelis MC, Tchetgen EJ, Liang L, Qi L, Chatterjee N, Hu FB, Kraft P. 2012. Gene-environment interactions in genome-wide association studies: a comparative study of tests applied to empirical studies of type 2 diabetes. Am J Epidemiol 175(3):191-202.
9. Davies JL, Hein J, Holmes CC. 2010. Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknown. Genet Epidemiol 34(4):299-308.
10. Demissie S, Cupples LA. 2011. Bias due to two-stage residual-outcome regression analysis in genetic association studies. Genet Epidemiol 35(7):592-596.
11. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. 2010. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11(6):446-450.
12. Evans DM, Marchini J, Morris AP, Cardon LR. 2006. Two-stage two-locus models in genome-wide association. PLoS Genet 2(9):e157.
13. Hamza TH, Chen H, Hill-Burns EM, Rhodes SL, Montimurro J, Kay DM, Tenesa A, Kusel VI, Sheehan P, Eaaswarkhanth M and others. 2011. Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee. PLoS Genet 7(8):e1002237.
14. Hirschhorn JN, Daly MJ. 2005. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6(2):95-108.
15. Hoh J, Wille A, Zee R, Cheng S, Reynolds R, Lindpaintner K, Ott J. 2000. Selecting SNPs in two-stage analysis of disease association data: a model-free approach. Ann Hum Genet 64(Pt 5):413-417.
16. Hunter DJ. 2005. Gene-environment interactions in human diseases. Nat Rev Genet 6(4):287-298.
17. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A and others. 2007. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39(7):870-874.
18. Kooperberg C, Leblanc M. 2008. Increasing the power of identifying gene x gene interactions in genome-wide association studies. Genet Epidemiol 32(3):255-263.
19. Kraft P, Yen YC, Stram DO, Morrison J, Gauderman WJ. 2007. Exploiting gene-environment interaction to detect genetic associations. Hum Hered 63(2):111-119.
20. Lindstrom S, Yen YC, Spiegelman D, Kraft P. 2009. The impact of gene-environment dependence and misclassification in genetic association studies incorporating gene-environment interactions. Hum Hered 68(3):171-181.
21. Lindstrom S, Vachon CM, Li J, Varghese J, Thompson D, Warren R, Brown J, Leyland J, Audley T, Wareham NJ and others. 2011. Common variants in ZNF365 are associated with both mammographic density and breast cancer risk. Nat Genet 43(3):185-187.
22. Mackay TF, Stone EA, Ayroles JF. 2009. The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10(8):565-577.
23. 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(7265):747-753.
24. Marchini J, Donnelly P, Cardon LR. 2005. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37(4):413-417.
25. McKinney BA, Reif DM, Ritchie MD, Moore JH. 2006. Machine learning for detecting gene-gene interactions: a review. Appl Bioinformatics 5(2):77-88.
26. 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. Carcinogenesis 29(6):1215-1218.
27. Mukherjee B, Ahn J, Gruber SB, Chatterjee N. 2012. Testing gene-environment interaction in large-scale case-control association studies: possible choices and comparisons. Am J Epidemiol 175(3):177-190.
28. Murcray CE, Lewinger JP, Gauderman WJ. 2009. Gene-environment interaction in genome-wide association studies. Am J Epidemiol 169(2):219-226.
29. O'Brien P. 1988. Comparing two samples: extensions of the t, rank-sum, and log-rank tests. J Am Stat Assoc 83(401):52-61.
30. Pare G, Cook NR, Ridker PM, Chasman DI. 2010. On the use of variance per genotype as a tool to identify quantitative trait interaction effects: a report from the Women's Genome Health Study. PLoS Genet 6(6):e1000981.
31. Phillips PC. 2008. Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9(11):855-867.
32. Reimherr M, Nicolae DL. 2010. You've gotta be lucky: coverage and the elusive gene-gene interaction. Ann Hum Genet 75(1):105-111.
33. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC. 2011. Detecting novel associations in large data sets. Science 334(6062):1518-1524.
34. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH. 2001. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69(1):138-147.
35. Takeuchi F, Kobayashi S, Ogihara T, Fujioka A, Kato N. 2011. Detection of common single nucleotide polymorphisms synthesizing quantitative trait association of rarer causal variants. Genome Res 21(7):1122-1130.
36. Tamimi RM, Cox DG, Kraft P, Pollak MN, Haiman CA, Cheng I, Freedman ML, Hankinson SE, Hunter DJ, Colditz GA. 2007. Common genetic variation in IGF1, IGFBP-1, and IGFBP-3 in relation to mammographic density: a cross-sectional study. Breast Cancer Res 9(1):R18.
37. Thomas D. 2010. Gene-environment-wide association studies: emerging approaches. Nat Rev Genet 11(4):259-272.
38. Xiao Y, Gordon A, Yakovlev A. 2006. A C++ program for the Cramér-Von Mises two-sample test. J Stat Softw 17(8).
39. Zeegers M, Rijsdijk F, Sham P. 2004. Adjusting for covariates in variance components QTL linkage analysis. Behav Genet 34(2):127-133.
40. Zhang Y, Liu JS. 2007. Bayesian inference of epistatic interactions in case-control studies. Nat Genet 39(9):1167-1173.