A hidden Markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping

Genetics

Volumn 184, Issue 3, 2010, Pages 789-798

  Druet, Tom ^a   Georges, Michel ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALLELE; ARTICLE; CHROMOSOME; CONTROLLED STUDY; EVALUATION; GENE CLUSTER; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENOTYPE; HAPLOTYPE; HIDDEN MARKOV MODEL; HUMAN; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; FEMALE; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MARKOV CHAINS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

ANIMALIA;

EID: 77950613737     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.109.108431     Document Type: Article

References (31)

1. Blott, S., J. J. Kim, S. Moisio, A. Schmidt-Kuntzel, A. Cornet et al. 2003 Molecular dissection of a quantitative trait locus: a phenylalanine-to- tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 163: 253-266.
2. Browning, B. L., and S. R. Browning, 2007 Efficient multilocus association testing for whole genome association studies using localized haplotype clustering. Genet. Epidemiol. 31: 365-375.
3. Browning, B. L., and S. R. Browning, 2009 A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 84: 210-223.
4. Browning, S. R., 2006 Multilocus association mapping using variable-length Markov chains. Am. J. Hum. Genet. 78: 903-913.
5. Browning, S. R., and B. L. Browning, 2007 Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81: 1084-1097.
6. Charlier, C., W. Coppieters, F. Rollin, D. Desmecht, J. S. Agerholm et al. 2008 Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat. Genet. 40: 449-454.
7. Druet, T., S. Fritz, M. Boussaha, S. Ben-Jemaa, F. Guillaume et al. 2008 Fine mapping of quantitative trait loci affecting female fertility in dairy cattle on BTA03 using a dense single-nucleotide polymorphism map. Genetics 178: 2227-2235.
8. George, A. W., P. M. Visscher and C. S. Haley, 2000 Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach. Genetics 156: 2081-2092.
9. Goddard, M.E., and B.J. Hayes, 2009 Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10(6): 381-391.
10. Grisart, B., W. Coppieters, F. Farnir, L. Karim, C. Ford et al. 2002 Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 12: 222-231.
11. Grisart, B., F. Farnir, L. Karim, N. Cambisano, J. J. Kim et al. 2004 Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proc. Natl. Acad. Sci. USA 101: 2398-2403.
12. Guo, S. W., 1994 Computation of identity-by-descent proportions shared by two siblings. Am. J. Hum. Genet. 54: 1104-1109.
13. Habier, D., R. L. Fernando and J. C. Dekkers, 2009 Genomic selection using low-density marker panels. Genetics 182: 343-353.
14. Hayes, B. J., A. J. Chamberlain and M. E. Goddard, 2006 Use of markers in linkage disequilibrium with QTL in breeding programs. Proceeding from the 8th World Congress of Genetics Applied to Livestock Production, Belo Horizonte, Brazil, August 13-18.
15. Henderson, C. R., 1984 Estimation of variances and covariances under multiple traits models. J. Dairy Sci. 67: 1581-1589.
16. Hudson, R. R., 2002 Generating samples under aWright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
17. Johnson, D. L., and R. Thompson, 1995 Restricted maximum likelihood estimation of variance components for univariate animal models using sparse matrix techniques and average information. J. Dairy Sci. 78: 449-456.
18. Kong, A., G. Masson, M. L. Frigge, A. Gylfason, P. Zusmanovich et al. 2008 Detection of sharing by descent, long-range phasing and haplotype imputation. Nat. Genet. 40: 1068-1075.
19. Marchini, J., B. Howie, S. Myers, G. McVean and P. Donnelly, 2007 A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39: 906-913.
20. Meuwissen, T. H., and M. E. Goddard, 2000 Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci. Genetics 155: 421-430.
21. Meuwissen, T. H., and M. E. Goddard, 2001 Prediction of identity by descent probabilities from marker-haplotypes. Genet. Sel. Evol. 33: 605-634.
22. Meuwissen, T. H., and M. E. Goddard, 2007 Multipoint identity-bydescent prediction using dense markers to map quantitative trait loci and estimate effective population size. Genetics 176: 2551-2560.
23. Meuwissen, T. H., B. J. Hayes and M. E. Goddard, 2001 Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
24. Rabiner, L. R., 1989 A tutorial on Hidden Markov Chains and selected applications in speech recognition. Proc. IEEE 77: 257-286.
25. Scheet, P., and M. Stephens, 2006 A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78: 629-644.
26. VanRaden, P. M., and G. R. Wiggans, 1991 Derivation, calculation, and use of national animal model information. J. Dairy Sci. 74: 2737-2746.
27. Van Tassell, C. P., T. P. Smith, L. K. Matukumalli, J. F. Taylor, R. D. Schnabel et al. 2008 SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 5: 247-252.
28. Voight, B.G., S. Kudaravalli, X. Wen and J.K. Pritchard, 2006 A map of recent positive selection in the human genome. PloS Biol. 4(3): e72.
29. Wellcome Trust Case Control Consortium, 2007 Genome wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 645-646.
30. Windig, J. J., and T. H. E. Meuwissen, 2004 Rapid haplotype reconstruction in pedigrees with dense marker maps. J. Anim. Breed. Genet. 121: 26-39.
31. Yu, J., J. B. Holland, M. D. McMullen and E. S. Buckler, 2008 Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.