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Volumn 28, Issue 19, 2012, Pages 2467-2473

Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; CATTLE; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; HAPLOTYPE; MALE; METHODOLOGY; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

EID: 84867315459     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts348     Document Type: Article
Times cited : (35)

References (37)
  • 1
    • 44249112333 scopus 로고    scopus 로고
    • A genomic background based method for association analysis in related individuals
    • Amin,N. et al. (2007) A genomic background based method for association analysis in related individuals. PLoS One, 2, e1274.
    • (2007) PLoS One , vol.2 , pp. 1274
    • Amin, N.1
  • 2
    • 33646443682 scopus 로고    scopus 로고
    • Genome-wide association mapping in arabidopsis identifies previously known flowering time and pathogen resistance genes
    • Aranzana,M.J. et al. (2005) Genome-wide association mapping in arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet., 1, e60.
    • (2005) PLoS Genet , vol.1
    • Aranzana, M.J.1
  • 3
    • 35048838105 scopus 로고    scopus 로고
    • Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis
    • Aulchenko,Y.S. et al. (2007) Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics, 177, 577-585.
    • (2007) Genetics , vol.177 , pp. 577-585
    • Aulchenko, Y.S.1
  • 4
    • 0037274657 scopus 로고    scopus 로고
    • 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
    • Blott,S. 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.
    • (2003) Genetics , vol.163 , pp. 253-266
    • Blott, S.1
  • 5
    • 0011241944 scopus 로고
    • Approximate inference in generalized linear mixed models
    • Breslow,N. and Clayton,D. (1993) Approximate inference in generalized linear mixed models. J. Am. Stat. Assoc., 88, 9-25.
    • (1993) J. Am. Stat. Assoc. , vol.88 , pp. 9-25
    • Breslow, N.1    Clayton, D.2
  • 6
    • 57049184635 scopus 로고    scopus 로고
    • Missing data imputation and haplotype phase inference for genome-wide association studies
    • Browning,S.R. (2008) Missing data imputation and haplotype phase inference for genome-wide association studies. Hum. Genet., 124, 439-450.
    • (2008) Hum. Genet. , vol.124 , pp. 439-450
    • Browning, S.R.1
  • 7
    • 35348817330 scopus 로고    scopus 로고
    • Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    • Browning,S.R. and Browning,B.L. (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.
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 1084-1097
    • Browning, S.R.1    Browning, B.L.2
  • 8
    • 0030074569 scopus 로고    scopus 로고
    • Microsatellite mapping of the bovine roan locus: a major determinant of white heifer disease
    • Charlier,C. et al. (1996) Microsatellite mapping of the bovine roan locus: a major determinant of white heifer disease. Mamm. Genome, 7, 138-142.
    • (1996) Mamm. Genome , vol.7 , pp. 138-142
    • Charlier, C.1
  • 9
    • 40849110768 scopus 로고    scopus 로고
    • Highly effective SNP-based association mapping and management of recessive defects in livestock
    • Charlier,C. et al. (2008) Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat. Genet., 40, 449-454.
    • (2008) Nat. Genet. , vol.40 , pp. 449-454
    • Charlier, C.1
  • 10
    • 80051726990 scopus 로고    scopus 로고
    • Genomic breeding value estimation using genetic markers, inferred ancestral haplotypes, and the genomic relationship matrix
    • de Roos,A.P.W. et al. (2011) Genomic breeding value estimation using genetic markers, inferred ancestral haplotypes, and the genomic relationship matrix. J. Dairy Sci., 94, 4708-4714.
    • (2011) J. Dairy Sci. , vol.94 , pp. 4708-4714
    • de Roos, A.P.W.1
  • 11
    • 0032714352 scopus 로고    scopus 로고
    • Genomic control for association studies
    • Devlin,B. and Roeder,K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
    • (1999) Biometrics , vol.55 , pp. 997-1004
    • Devlin, B.1    Roeder, K.2
  • 12
    • 57649136554 scopus 로고    scopus 로고
    • Progress and challenges in genome-wide association studies in humans
    • Donnelly,P. (2008) Progress and challenges in genome-wide association studies in humans. Nature, 456, 728-731.
    • (2008) Nature , vol.456 , pp. 728-731
    • Donnelly, P.1
  • 13
    • 77950613737 scopus 로고    scopus 로고
    • A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping
    • Druet,T. and Georges,M. (2010) A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. Genetics, 184, 789-798.
    • (2010) Genetics , vol.184 , pp. 789-798
    • Druet, T.1    Georges, M.2
  • 14
    • 45849144059 scopus 로고    scopus 로고
    • Fine mapping of quantitative trait loci affecting female fertility in dairy cattle on BTA03 using a dense single-nucleotide polymorphism map
    • Druet,T. 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.
    • (2008) Genetics , vol.178 , pp. 2227-2235
    • Druet, T.1
  • 15
    • 84863043816 scopus 로고    scopus 로고
    • Serial translocation via circular intermediates underlies color-sidedness in cattle
    • Durkin,K. et al. (2012) Serial translocation via circular intermediates underlies color-sidedness in cattle. Nature, 482, 81-84.
    • (2012) Nature , vol.482 , pp. 81-84
    • Durkin, K.1
  • 16
    • 3042591234 scopus 로고    scopus 로고
    • Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes
    • Durrant,C. et al. (2004) Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. Am. J. Hum. Genet., 75, 35-43.
    • (2004) Am. J. Hum. Genet. , vol.75 , pp. 35-43
    • Durrant, C.1
  • 17
    • 1842740737 scopus 로고    scopus 로고
    • Marker-based estimates of between and within population kinships for the conservation of genetic diversity
    • Eding,H. et al. (2001) Marker-based estimates of between and within population kinships for the conservation of genetic diversity. J. Anim. Breed. Genet., 118, 141-159.
    • (2001) J. Anim. Breed. Genet. , vol.118 , pp. 141-159
    • Eding, H.1
  • 18
    • 0034532484 scopus 로고    scopus 로고
    • Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach
    • George,A.W. et al. (2000) Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach. Genetics, 156, 2081-2092.
    • (2000) Genetics , vol.156 , pp. 2081-2092
    • George, A.W.1
  • 19
    • 52649102962 scopus 로고    scopus 로고
    • Technical note: prediction of breeding values using marker-derived relationship matrices
    • Hayes,B.J. and Goddard,M.E. (2008) Technical note: prediction of breeding values using marker-derived relationship matrices. J. Anim. Sci., 86, 2089-2092.
    • (2008) J. Anim. Sci. , vol.86 , pp. 2089-2092
    • Hayes, B.J.1    Goddard, M.E.2
  • 20
    • 45149105926 scopus 로고    scopus 로고
    • Efficient control of population structure in model organism association mapping
    • Kang,H.M. et al. (2008) Efficient control of population structure in model organism association mapping. Genetics, 178, 1709-1723.
    • (2008) Genetics , vol.178 , pp. 1709-1723
    • Kang, H.M.1
  • 21
    • 77950301214 scopus 로고    scopus 로고
    • Variance component model to account for sample structure in genome-wide association studies
    • Kang,H.M. et al. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat. Genet., 42, 348-354.
    • (2010) Nat. Genet. , vol.42 , pp. 348-354
    • Kang, H.M.1
  • 22
    • 85017471807 scopus 로고    scopus 로고
    • Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature
    • Karim,L. et al. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat. Genet., 43, 405-413.
    • (2011) Nat. Genet. , vol.43 , pp. 405-413
    • Karim, L.1
  • 23
    • 34247853365 scopus 로고    scopus 로고
    • A mixed-model approach to association mapping using pedigree information with an illustration of resistance to phytophthora infestans in potato
    • Malosetti,M. et al. (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to phytophthora infestans in potato. Genetics, 175, 879-889.
    • (2007) Genetics , vol.175 , pp. 879-889
    • Malosetti, M.1
  • 25
    • 0035543447 scopus 로고    scopus 로고
    • Prediction of identity by descent probabilities from marker-haplotypes
    • Meuwissen,T.H. and Goddard,M.E. (2001) Prediction of identity by descent probabilities from marker-haplotypes. Genet. Sel. Evol., 33, 605-634.
    • (2001) Genet. Sel. Evol. , vol.33 , pp. 605-634
    • Meuwissen, T.H.1    Goddard, M.E.2
  • 26
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • Price,A.L. et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
    • (2006) Nat. Genet. , vol.38 , pp. 904-909
    • Price, A.L.1
  • 27
    • 0033926805 scopus 로고    scopus 로고
    • Association mapping in structured populations
    • Pritchard,J.K. et al. (2000) Association mapping in structured populations. Am. J. Hum. Genet., 67, 170-181.
    • (2000) Am. J. Hum. Genet. , vol.67 , pp. 170-181
    • Pritchard, J.K.1
  • 28
    • 84859222356 scopus 로고    scopus 로고
    • A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory response
    • Sartelet,A. et al. (2012) A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory response. PLoS Genet., 8, e1002581.
    • (2012) PLoS Genet , vol.8
    • Sartelet, A.1
  • 29
    • 0036155283 scopus 로고    scopus 로고
    • Score tests for association between traits and haplotypes when linkage phase is ambiguous
    • Schaid,D.J. et al. (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am. J. Hum. Genet., 70, 425-434.
    • (2002) Am. J. Hum. Genet. , vol.70 , pp. 425-434
    • Schaid, D.J.1
  • 30
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for largescale population genotype data: applications to inferring missing genotypes and haplotypic phase
    • Scheet,P. and Stephens,M. (2006) A fast and flexible statistical model for largescale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet., 78, 629-644.
    • (2006) Am. J. Hum. Genet. , vol.78 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 31
    • 0038449167 scopus 로고    scopus 로고
    • Evolutionary-based association analysis using haplotype data
    • Seltman,H. et al. (2003) Evolutionary-based association analysis using haplotype data. Genet. Epidemiol., 25, 48-58.
    • (2003) Genet. Epidemiol. , vol.25 , pp. 48-58
    • Seltman, H.1
  • 32
    • 41349095907 scopus 로고    scopus 로고
    • Disease association tests by inferring ancestral haplotypes using a hidden Markov model
    • Su,S.-Y. et al. (2008) Disease association tests by inferring ancestral haplotypes using a hidden Markov model. Bioinformatics, 24, 972-978.
    • (2008) Bioinformatics , vol.24 , pp. 972-978
    • Su, S.-Y.1
  • 33
    • 0036215090 scopus 로고    scopus 로고
    • Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort
    • Threadgill,D.W. et al. (2002) Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mamm. Genome, 13, 175-178.
    • (2002) Mamm. Genome , vol.13 , pp. 175-178
    • Threadgill, D.W.1
  • 34
    • 35348887757 scopus 로고    scopus 로고
    • Haplotype-based association analysis via variance components score test
    • Tzeng,J.-Y. and Zhang,D. (2007) Haplotype-based association analysis via variance components score test. Am. J. Hum. Genet., 81, 927-938.
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 927-938
    • Tzeng, J.-Y.1    Zhang, D.2
  • 35
    • 0037531799 scopus 로고    scopus 로고
    • The use of score tests for inference on variance components
    • Verbeke,G. and Molenberghs,G. (2003) The use of score tests for inference on variance components. Biometrics, 59, 254-262.
    • (2003) Biometrics , vol.59 , pp. 254-262
    • Verbeke, G.1    Molenberghs, G.2
  • 36
    • 31744440502 scopus 로고    scopus 로고
    • A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    • Yu,J. et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet., 38, 203-208.
    • (2006) Nat. Genet. , vol.38 , pp. 203-208
    • Yu, J.1
  • 37
    • 33846466407 scopus 로고    scopus 로고
    • An Arabidopsis example of association mapping in structured samples
    • Zhao,K. et al. (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet., 3, e4.
    • (2007) PLoS Genet , vol.3
    • Zhao, K.1


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