Reconciling the analysis of IBD and IBS in complex trait studies (original) (raw)
Malécot, G. Les Mathématiques de l'Hérédité. (Masson, Paris, 1948). Google Scholar
Wright, S. Coefficients of inbreeding and relationship. Am. Nat.51, 636–639 (1917). Article Google Scholar
Wright, S. Systems of mating. I. The biometric relations between parent and offspring. Genetics6, 111–123 (1921). CASPubMedPubMed Central Google Scholar
Kong, A. et al. Detection of sharing by descent, long-range phasing and haplotype imputation. Nature Genet.40, 1068–1075 (2008). ArticleCASPubMed Google Scholar
Albrechtsen, A. et al. Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium. Genet. Epidemiol.33, 266–274 (2009). ArticlePubMed Google Scholar
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet.81, 559–575 (2007). ArticleCASPubMedPubMed Central Google Scholar
Visscher, P. M. et al. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet.2, 316–325 (2006). ArticleCAS Google Scholar
Charlesworth, D. & Willis, J. H. The genetics of inbreeding depression. Nature Rev. Genet.10, 783–796 (2009). ArticleCASPubMed Google Scholar
The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature449, 851–862 (2007).
Hartl, D. L. & Clark, A. G. Principles of Population Genetics (Sinauer Associates, Massachusetts, 1997). Google Scholar
Rosenberg, N. A. & Nordborg, M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Rev. Genet.3, 380–390 (2002). ArticleCASPubMed Google Scholar
Nordborg, M. in Handbook of Statistical Genetics (eds Balding, D. J., Bishop, M. & Cannings, C.) 179–212 (Wiley, Chichester, 2001). Google Scholar
Browning, S. R. Estimation of pairwise identity by descent from dense genetic marker data in a population sample of haplotypes. Genetics178, 2123–2132 (2008). ArticlePubMedPubMed Central Google Scholar
Lynch, M. & Walsh, B. Genetics and Analysis of Quantitative Traits (Sinauer Associates, Massachusetts, 1998). Google Scholar
Jacquard, A. The Genetic Structure of Populations (Springer, New York, 1974). Book Google Scholar
Hayes, B. J., Visscher, P. M., McPartlan, H. C. & Goddard, M. E. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res.13, 635–643 (2003). ArticleCASPubMedPubMed Central Google Scholar
Astle, W. & Balding, D. J. Population structure and cryptic relatedness in genetic association studies. Stat. Sci.24, 451–471 (2009). Article Google Scholar
Yang, J. et al. Common SNPs explain a large proportion of the heritability for human. Nature Genet.42, 565–571 (2010). ArticleCASPubMed Google Scholar
Chadeau-Hyam, M. et al. Fregene: simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics9, 364–375 (2008). ArticlePubMedPubMed Central Google Scholar
Visscher, P. M., Hill, W. G. & Wray, N. R. Heritability in the genomics era — concepts and misconceptions. Nature Rev. Genet.9, 255–266 (2008). ArticleCASPubMed Google Scholar
Meuwissen, T. H. E., Hayes, B. J. & Goddard, M. E. Prediction of total genetic value using genome-wide dense marker maps. Genetics157, 1819–1829 (2001). CASPubMedPubMed Central Google Scholar
Hayes, B. J., Visscher, P. M. & Goddard, M. E. Increased accuracy of artificial selection by using the realized relationship matrix. Genet. Res.91, 47–60 (2009). ArticleCAS Google Scholar
Goddard, M. E. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica136, 245–257 (2009). ArticlePubMed Google Scholar
Habier, D., Fernando, R. L. & Dekkers, J. C. The impact of genetic relationship information on genome-assisted breeding values. Genetics177, 2389–2397 (2008). Article Google Scholar
VanRaden, P. M. Efficient methods to compute genomic predictions. J. Dairy Sci.91, 4414–4423 (2008). ArticleCASPubMed Google Scholar
Goddard, M. E. & Meuwissen, T. H. E. The use of linkage disequilibrium to map quantitative trait loci. Aust. J. Exp. Agric.45, 837–845 (2005). ArticleCAS Google Scholar
Meuwissen, T. H. E. & Goddard, M. E. Multipoint identity-by-descent prediction using dense markers to map quantitative trait loci and estimate effective population size. Genetics176, 2551–2560 (2007). ArticleCASPubMedPubMed Central Google Scholar
Lander, E. S. & Botstein D. Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science236, 1567–1570 (1987). ArticleCASPubMed Google Scholar
Lynch, M. & Ritland, K. Estimation of pairwise relatedness with molecular markers. Genetics152, 1753–1766 (1999). CASPubMedPubMed Central Google Scholar
Carothers, A. D. et al. Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. Ann. Hum. Genet.70, 666–676 (2006). ArticleCASPubMed Google Scholar
Charlesworth, B. & Charlesworth, D. The genetic basis of inbreeding depression. Genet. Res.74, 571–576 (1999). Article Google Scholar
Broman, K. W. & Weber, J. L. Long homozygous chromosome segments in reference families from the centre d'étude du polymorphisme humain. Am. J. Hum. Genet.65, 1493–1500 (1999). ArticleCASPubMedPubMed Central Google Scholar
Hayes, B. J., Bowman, P. J., Chamberlain, A. C., Verbyla, K. & Goddard, M. E. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet. Sel. Evol.41, 51 (2009). ArticlePubMedPubMed Central Google Scholar
Goddard, M. E., Wray, N. R., Verbyla, K. & Visscher, P. M. Estimating effects and making predictions from genome-wide marker data. Stat. Sci.24, 517–529 (2009). Article Google Scholar