Estimation of epistatic variance components and heritability in founder populations and crosses

Genetics

Volumn 198, Issue 4, 2014, Pages 1405-1416

  Young, Alexander I ^a   Durbin, Richard ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COVARIANCE; CROSS BREEDING; EPISTASIS; EPISTATIC VARIANCE; GENE FREQUENCY; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HERITABILITY; HUMAN; INBREEDING; INBREEDING DEPRESSION; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PHENOTYPE; POPULATION GENETICS; SACCHAROMYCES CEREVISIAE; SIMULATION; VARIANCE; YEAST; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; FOUNDER EFFECT; GENETICS; INHERITANCE; QUANTITATIVE TRAIT; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; CROSSES, GENETIC; EPISTASIS, GENETIC; FOUNDER EFFECT; GENETIC VARIATION; GENETICS, POPULATION; INHERITANCE PATTERNS; MODELS, GENETIC; MODELS, STATISTICAL; PHENOTYPE; QUANTITATIVE TRAIT, HERITABLE; YEASTS;

EID: 84915781695     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.170795     Document Type: Article

References (37)

1. Abney, M., M. S. McPeek, and C. Ober, 2000 Estimation of variance components of quantitative traits in inbred populations. Am. J. Hum. Genet. 66: 629-650.
2. Anderson, J. B., J. Funt, D. A. Thompson, S. Prabhu, A. Socha et al., 2010 Determinants of divergent adaptation and Dobzhansky- Muller interaction in experimental yeast populations. Curr. Biol. 20: 1383-1388.
3. Baud, A., R. Hermsen, V. Guryev, P. Stridh, D. Graham et al., 2013 Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nat. Genet. 45: 767-775.
4. Bloom, J. S., I. M. Ehrenreich, W. T. Loo, T.-L. V. o. Lite, and L. Kruglyak, 2013 Finding the sources of missing heritability in a yeast cross. Nature 494: 234-237.
5. Boomsma, D., A. Busjahn, and L. Peltonen, 2002 Classical twin studies and beyond. Nat. Rev. Genet. 3: 872-882.
6. Brown, A. A., A. Buil, A. Viñuela, T. Lappalainen, H.-f. Zheng et al., 2014 Genetic interactions affecting human gene expression identified by variance association mapping. eLife 3: e01381.
7. Browning, S. R., and B. L. Browning, 2013 Identity-by-descentbased heritability analysis in the Northern Finland Birth Cohort. Hum. Genet. 132: 129-138.
8. Carmi, S., P. F. Palamara, V. Vacic, T. Lencz, A. Darvasi et al., 2013 The variance of identity-by-descent sharing in the Wright-Fisher model. Genetics 193: 911-928.
9. Cockerham, C. C., 1954 An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39: 859-882.
10. Cockerham, C. C., and H. Tachida, 1988 Permanency of response to selection for quantitative characters in finite populations. Proc. Natl. Acad. Sci. USA 85: 1563-1565.
11. Eichler, E. E., J. Flint, G. Gibson, A. Kong, S. M. Leal et al., 2010 Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet. 11: 446-450.
12. Fisher, R., 1918 The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinb. 52: 399-433.
13. Gallais, A., 1974 Covariances between arbitrary relatives with linkage and epistasis in the case of linkage disequilibrium. Biometrics 30: 429-446.
14. Gauvin, H., C. Moreau, J.-F. Lefebvre, C. Laprise, H. Vézina, et al., 2013 Genome-wide patterns of identity-by-descent sharing in the French Canadian founder population. Eur. J. Hum. Genet. 22: 814-821.
15. Gilmour, A. R., R. Thompson, and B. R. Cullis, 1995 Average information REML: an efficient algorithm for variance parameter estimation in linear mixed models. Biometrics 51: 1440- 1450.
16. Hemani, G., S. Knott, and C. Haley, 2013 An evolutionary perspective on epistasis and the missing heritability. PLoS Genet. 9: e1003295.
17. Hemani, G., K. Shakhbazov, H.-J. Westra, T. Esko, A. K. Henders et al., 2014 Detection and replication of epistasis influencing transcription in humans. Nature 508: 249-253.
18. Hill, W. G., M. E. Goddard, and P. M. Visscher, 2008 Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet. 4: e1000008.
19. Kempthorne, O., 1954 The correlation between relatives in a random mating population. Proc. R. Soc. Lond. B Biol. Sci. 143: 103-113.
20. Kempthorne, O., 1955 The theoretical values of correlations between relatives in random mating populations. Genetics 40: 153-167.
21. Khoury, M. J., B. H. Cohen, E. L. Diamond, G. A. Chase, and V. A. McKusick, 1987 Inbreeding and prereproductive mortality in the Old Order Amish. I. Genealogic epidemiology of inbreeding. Am. J. Epidemiol. 125: 453-461.
22. Liti, G., D. M. Carter, A. M. Moses, J. Warringer, L. Parts et al., 2009 Population genomics of domestic and wild yeasts. Nature 458: 337-341.
23. Mackay, T. F. C., 2014 Epistasis and quantitative traits: using model organisms to study gene-gene interactions. Nat. Rev. Genet. 15: 22-33.
24. Nelson, R. M., M. E. Pettersson, X. Li, andO. Carlborg, 2013 Variance heterogeneity in Saccharomyces cerevisiae expression data: transregulation and epistasis. PLoS ONE 8: e79507.
25. Orr, H. A., 1995 The population genetics of speciation: the evolution of hybrid incompatibilities. Genetics 139: 1805-1813.
26. Pettersson, M., F. Besnier, P. B. Siegel, and O. Carlborg, 2011 Replication and explorations of high-order epistasis using a large advanced intercross line pedigree. PLoS Genet. 7: e1002180.
27. Speed, D., G. Hemani, M. R. Johnson, and D. J. Balding, 2012 Improved heritability estimation from genome-wide SNPs. Am. J. Hum. Genet. 91: 1011-1021.
28. Strange, A., F. Capon, C. C. A. Spencer, J. Knight, M. E. Weale et al., 2010 A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat. Genet. 42: 985-990.
29. Tachida, H., and C. C. Cockerham, 1989 Effects of identity disequilibrium and linkage on quantitative variation in finite populations. Genet. Res. 53: 63-70.
30. Taylor, M. B., and I. M. Ehrenreich, 2014 Genetic interactions involving five or more genes contribute to a complex trait in yeast. PLoS Genet. 10: e1004324.
31. Visscher, P. M., S. E. Medland, M. R. Ferreira, K. I. Morley, G. Zhu et al., 2006 Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet. 2: e41.
32. Visscher, P. M., M. A. Brown, M. I. McCarthy, and J. Yang, 2012 Five years of GWAS discovery. Am. J. Hum. Genet. 90: 7-24.
33. Vukcevic, D., E. Hechter, C. Spencer, and P. Donnelly, 2011 Disease model distortion in association studies. Genet. Epidemiol. 290: 278-290.
34. Yang, J., B. Benyamin, B. P. McEvoy, S. Gordon, A. K. Henders et al., 2010 Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42: 565-569.
35. Yang, J., S. H. Lee, M. E. Goddard, and P. M. Visscher, 2011 GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88: 76-82.
36. Zaitlen, N., P. Kraft, N. Patterson, B. Pasaniuc, G. Bhatia et al., 2013 Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. PLoS Genet. 9: e1003520.
37. Zuk, O., E. Hechter, S. R. Sunyaev, and E. S. Lander, 2012 The mystery of missing heritability: genetic interactions create phantom heritability. Proc. Natl. Acad. Sci. USA 109: 1193-1198.