Assumptions and Properties of Limiting Pathway Models for Analysis of Epistasis in Complex Traits

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Stringer, Sven ^a,b,c   Derks, Eske M ^a   Kahn, René S ^b   Hill, William G ^d   Wray, Naomi R ^c  

^a ACADEMIC MEDICAL CENTER   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; EPISTASIS; FEMALE; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC VARIABILITY; HERITABILITY; HUMAN; LIMITING PATHWAY MODEL; MALE; PHENOTYPE; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; EPISTASIS, GENETIC; FEMALE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MODELS, GENETIC; MULTIFACTORIAL INHERITANCE; PHENOTYPE; QUANTITATIVE TRAIT, HERITABLE; TWINS;

EID: 84880836251     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068913     Document Type: Article

References (49)

1. Maher B, (2008) The case of the missing heritability. Nature 456: 18-21.
2. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
3. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11: 446-450.
4. Clarke AJ, Cooper DN, (2010) GWAS: heritability missing in action? Eur J Hum Genet 18: 859-861.
5. Stringer S, Wray NR, Kahn RS, Derks EM, (2011) Underestimated effect sizes in GWAS: fundamental limitations of single SNP analysis for dichotomous phenotypes. PLoS ONE 6: e27964.
6. Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edition. Harlow, Essex: Longmans Green.
7. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sunderland, MA: Sinauer Associates.
8. Visscher PM, Hill WG, Wray NR, (2008) Heritability in the genomics era- concepts and misconceptions. Nat Rev Genet 9: 255-266.
9. Sham P (1998) Statistics in Human Genetics. London: Wiley.
10. Haenszel W, (1959) Some problems in the estimation of familial risks of disease. J Natl Cancer Inst 23: 487-505.
11. Guo SW, (1998) Inflation of sibling recurrence-risk ratio, due to ascertainment bias and/or overreporting. Am J Hum Genet 63: 252-258.
12. Wray NR, Gottesman II, (2012) Using summary data from the Danish national registers to estimate heritabilities for schizophrenia, bipolar disorder, and major depressive disorder. Front Genet 3: 1-12.
13. Zuk O, Hechter E, Sunyaev SR, Lander ES, (2012) The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A 109: 1193-1198.
14. Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, et al. (2006) Variability and memory of protein levels in human cells. Nature 444: 643-646.
15. Hill WG, Zhang XS, (2012) On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms. Genetics 190: 1131-1137.
16. Mackay TFC, (2010) Mutations and quantitative genetic variation: lessons from Drosophila. Philos T Roy Soc B 365: 1229-1239.
17. van Dongen J, Slagboom PE, Draisma HHM, Martin NG, Boomsma DI, (2012) The continuing value of twin studies in the omics era. Nat Rev Genet 13: 640-653.
18. Silventoinen K, (2003) Determinants of variation in adult body height. J Biosoc Sci 35: 263-285.
19. Rahman I, Bennet AM, Pedersen NL, de Faire U, Svensson P, et al. (2009) Genetic dominance influences blood biomarker levels in a sample of 12,000 Swedish elderly twins. Twin Res Hum Genet 12: 286-294.
20. Teucher B, Skinner J, Skidmore PML, Cassidy A, Fairweather-Tait SJ, et al. (2007) Dietary patterns and heritability of food choice in a UK female twin cohort. Twin Res Hum Genet 10: 734-748.
21. Hill WG, Goddard ME, Visscher PM, (2008) Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet 4: e1000008.
22. Petersen L, Sørensen TIA, (2011) The Danish adoption register. Scand J Public Health 39: 83-86.
23. Wright S, (1935) The analysis of variance and the correlations between relatives with respect to deviations from an optimum. J Genet 30: 243-256.
24. Barton NH, Keightley PD, (2002) Understanding quantitative genetic variation. Nat Rev Genet 3: 11-21.
25. Carlborg O, Haley CS, (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
26. Phillips PC, (2008) Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
27. Hemani G, Knott S, Haley C, (2013) An evolutionary perspective on epistasis and the missing heritability. PLoS Genet 9: e1003295.
28. Crow JF, (2008) Maintaining evolvability. J Genet 87: 349-353.
29. Eyre-Walker A, (2010) Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. Proc Natl Acad Sci U S A 107: 1752-1756.
30. Mackay TF, Lyman RF, (2005) Drosophila bristles and the nature of quantitative genetic variation. Philos Trans R Soc Lond B Biol Sci 360: 1513-1527.
31. Huang W, Richards S, Carbone MA, Zhu D, Anholt RRH, et al. (2012) Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci U S A 109: 15553-15559.
32. Mackay TFC, Richards S, Stone EA, Barbadilla A, Ayroles JF, et al. (2012) The drosophila melanogaster genetic reference panel. Nature 482: 173-178.
33. Kacser H, Burns JA, (1979) Molecular democracy: Who shares the controls? Biochem Soc Trans 7: 1149-1160.
34. Suarez RK, Moyes CD, (2012) Metabolism in the age of 'omes'. J Exp Biol 215: 2351-2357.
35. Fell DA, (1992) Metabolic control analysis: experimental development of its theoretical and experimental development. Biochem J 286: 313-330.
36. Keightley PD, (1989) Models of quantitative variation of flux in metabolic pathways. Genetics 121: 869-876.
37. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
38. Lee SH, Wray NR, Goddard ME, Visscher PM, (2011) Estimating missing heritability for disease from genome-wide association studies. Am J Hum Genet 88: 294-305.
39. Yang J, Lee SH, Goddard ME, Visscher PM, (2011) GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 88: 76-82.
40. Zaitlen N, Kraft P, (2012) What psychiatric genetics has taught us about the nature of psychiatric illness and what is left to learn. Hum Genet 131: 1655-1664.
41. Visscher PM, Brown MA, McCarthy MI, Yang J, (2012) Five years of GWAS discovery. Am J Hum Genet 90: 7-24.
42. The Welcome 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.
43. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, et al. (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491: 119-124.
44. Bloom JS, Ehrenreich IM, Loo WT, Lite TLV, Kruglyak L, (2013) Finding the sources of missing heritability in a yeast cross. Nature 494: 234-237.
45. Kemper KE, Goddard ME, (2012) Understanding and predicting complex traits: knowledge from cattle. Hum Mol Genet 21: R45-R51.
46. Haile-Mariam M, Nieuwhof G, Beard K, Konstatinov K, Hayes B, (2013) Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations. J Anim Breed Genet 130: 20-31.
47. Michailidou K, Hall P, Gonzalez-Neira A, Ghoussaini M, Dennis J, et al. (2013) Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Nat Genet 45: 353-361.
48. Kendler KS (2013) What psychiatric genetics has taught us about the nature of psychiatric illness and what is left to learn. Mol Psychiatry. doi: 10.1038/mp.2013.50.
49. Visscher PM, Goddard ME, (2010) Systems genetics: the added value of gene expression. HFSP J 4: 6-10.