메뉴 건너뛰기




Volumn 198, Issue 1, 2014, Pages 139-156

Bayesian modeling of haplotype effects in multiparent populations

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CHOLESTEROL BLOOD LEVEL; CHROMOSOME 1; CHROMOSOME 10; CHROMOSOME 15; DIPLOIDY; DIPLOTYPE; EFFECT SIZE; ENTROPY; FOLLOW UP; GENE LOCUS; GENETIC HETEROGENEITY; GENETIC PARAMETERS; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; MOUSE; NONHUMAN; PEDIGREE; PHENOTYPE; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; SAMPLE SIZE; SIMULATION; UNCERTAINTY; ANIMAL; BIOLOGICAL MODEL; INBRED MOUSE STRAIN;

EID: 84907912911     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.166249     Document Type: Article
Times cited : (29)

References (57)
  • 1
    • 79957658264 scopus 로고    scopus 로고
    • Genetic analysis of complex traits in the emerging Collaborative Cross
    • Aylor, D. L., W. Valdar, W. Foulds-Mathes, R. J. Buus, R. A. Verdugo et al., 2011 Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res. 21(8): 1213–1222.
    • (2011) Genome Res , vol.21 , Issue.8 , pp. 1213-1222
    • Aylor, D.L.1    Valdar, W.2    Foulds-Mathes, W.3    Buus, R.J.4    Verdugo, R.A.5
  • 2
    • 84878774677 scopus 로고    scopus 로고
    • Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding
    • Bandillo, N., C. Raghavan, P. A. Muyco, M. A. L. Sevilla, I. T. Lobina et al., 2013 Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6(1): 11.
    • (2013) Rice , vol.6 , Issue.1 , pp. 11
    • Bandillo, N.1    Raghavan, C.2    Muyco, P.A.3    Sevilla, M.A.L.4    Lobina, I.T.5
  • 3
    • 84879692177 scopus 로고    scopus 로고
    • Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nat
    • 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(7): 767–775.
    • (2013) Genet , vol.45 , Issue.7 , pp. 767-775
    • Baud, A.1    Hermsen, R.2    Guryev, V.3    Stridh, P.4    Graham, D.5
  • 6
    • 41149121474 scopus 로고    scopus 로고
    • From mutations to MAGIC: Resources for gene discovery, validation and delivery in crop plants
    • Cavanagh, C., M. Morell, I. Mackay, and W. Powell, 2008 From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr. Opin. Plant Biol. 11(2): 215–221.
    • (2008) Curr. Opin. Plant Biol , vol.11 , Issue.2 , pp. 215-221
    • Cavanagh, C.1    Morell, M.2    Mackay, I.3    Powell, W.4
  • 7
    • 14644441018 scopus 로고    scopus 로고
    • The Collaborative Cross, a community resource for thegenetic analysis of complex traits. Nat
    • Churchill, G. A., D. C. Airey, H. Allayee, J. M. Angel, A. D. Attie et al., 2004 The Collaborative Cross, a community resource for thegenetic analysis of complex traits. Nat. Genet. 36(11): 1133–1137.
    • (2004) Genet , vol.36 , Issue.11 , pp. 1133-1137
    • Churchill, G.A.1    Airey, D.C.2    Allayee, H.3    Angel, J.M.4    Attie, A.D.5
  • 8
    • 84863115856 scopus 로고    scopus 로고
    • The genome architecture of the Collaborative Cross mouse genetic reference population
    • Collaborative Cross Consortium
    • Collaborative Cross Consortium, 2012 The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190: 389–401.
    • (2012) Genetics , vol.190 , pp. 389-401
  • 9
    • 77950625929 scopus 로고    scopus 로고
    • Bayesian quantitative trait locus mapping using inferred haplotypes
    • Durrant, C., and R. Mott, 2010 Bayesian quantitative trait locus mapping using inferred haplotypes. Genetics 184: 839–852.
    • (2010) Genetics , vol.184 , pp. 839-852
    • Durrant, C.1    Mott, R.2
  • 10
    • 84880944577 scopus 로고    scopus 로고
    • Modeling host genetic regulation of influenza pathogenesis in the collaborative cross
    • Ferris, M. T., D. L. Aylor, D. Bottomly, A. C. Whitmore, L. D. Aicher et al., 2013 Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. PLoS Pathog. 9(2): e1003196.
    • (2013) PLoS Pathog , vol.9 , Issue.2
    • Ferris, M.T.1    Aylor, D.L.2    Bottomly, D.3    Whitmore, A.C.4    Aicher, L.D.5
  • 11
    • 77950537175 scopus 로고    scopus 로고
    • Regularization paths for generalized linear models via coordinate descent
    • Friedman, J., T. Hastie, and R. Tibshirani, 2010 Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33(1): 1.
    • (2010) J. Stat. Softw , vol.33 , Issue.1 , pp. 1
    • Friedman, J.1    Hastie, T.2    Tibshirani, R.3
  • 14
    • 33646942472 scopus 로고
    • A simple regression method for mapping quantitative trait loci in line crosses using flanking markers
    • Haley, C. S., and S. A. Knott, 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69(4): 315–324.
    • (1992) Heredity , vol.69 , Issue.4 , pp. 315-324
    • Haley, C.S.1    Knott, S.A.2
  • 15
    • 84942484786 scopus 로고
    • Ridge regression: Biased estimation for nonorthogonal problems
    • Hoerl, A. E., and R. W. Kennard, 1970 Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12(1): 55–67.
    • (1970) Technometrics , vol.12 , Issue.1 , pp. 55-67
    • Hoerl, A.E.1    Kennard, R.W.2
  • 16
    • 79951983365 scopus 로고    scopus 로고
    • R/mpMap: A computational platform for the genetic analysis of multiparent recombinant inbred lines
    • Huang, B. E., and A. W. George, 2011 R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines. Bioinformatics 27(5): 727–729.
    • (2011) Bioinformatics , vol.27 , Issue.5 , pp. 727-729
    • Huang, B.E.1    George, A.W.2
  • 17
    • 84864509188 scopus 로고    scopus 로고
    • A multiparent advanced generation inter-cross population for genetic analysis in wheat
    • Huang, B. E., A. W. George, K. L. Forrest, A. Kilian, M. J. Hayden et al., 2012 A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol. J. 10(7): 826–839.
    • (2012) Plant Biotechnol. J , vol.10 , Issue.7 , pp. 826-839
    • Huang, B.E.1    George, A.W.2    Forrest, K.L.3    Kilian, A.4    Hayden, M.J.5
  • 18
    • 66449134529 scopus 로고    scopus 로고
    • High resolution mapping of expression QTLs in  heterogeneous stock mice in multiple tissues
    • Huang, G.-J., S. Shifman, W. Valdar, M. Johannesson, B. Yalcin et al., 2009 High resolution mapping of expression QTLs in  heterogeneous stock mice in multiple tissues. Genome Res. 19(6):1133–1140.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1133-1140
    • Huang, G.-J.1    Shifman, S.2    Valdar, W.3    Johannesson, M.4    Yalcin, B.5
  • 19
    • 79952719931 scopus 로고    scopus 로고
    • Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population
    • Huang, X., M.-J. Paulo, M. Boer, S. Effgen, P. Keizer et al., 2011 Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc. Natl. Acad. Sci. USA 108(11): 4488–4493.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , Issue.11 , pp. 4488-4493
    • Huang, X.1    Paulo, M.-J.2    Boer, M.3    Effgen, S.4    Keizer, P.5
  • 20
    • 61449224751 scopus 로고    scopus 로고
    • A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH heterogeneous stock
    • Johannesson, M., R. Lopez-Aumatell, P. Stridh, M. Diez, J. Tuncel et al., 2009 A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: the NIH heterogeneous stock. Genome Res. 19(1): 150–158.
    • (2009) Genome Res , vol.19 , Issue.1 , pp. 150-158
    • Johannesson, M.1    Lopez-Aumatell, R.2    Stridh, P.3    Diez, M.4    Tuncel, J.5
  • 21
    • 45149105926 scopus 로고    scopus 로고
    • Efficient control of population structure in model organism association mapping
    • Kang, H. M., N. A. Zaitlen, C. M. Wade, A. Kirby, D. Heckerman 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    Zaitlen, N.A.2    Wade, C.M.3    Kirby, A.4    Heckerman, D.5
  • 23
    • 0026888884 scopus 로고
    • Estimation of effects of single genes on quantitative traits
    • Kennedy, B.W., M. Quinton, and J. A. van Arendonk, 1992 Estimation of effects of single genes on quantitative traits. J. Anim. Sci. 70(7): 2000–2012.
    • (1992) J. Anim. Sci , vol.70 , Issue.7 , pp. 2000-2012
    • Kennedy, B.W.1    Quinton, M.2    Van Arendonk, J.A.3
  • 24
    • 84863868317 scopus 로고    scopus 로고
    • Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    • King, E. G., C. M. Merkes, C. L. McNeil, S. R. Hoofer, S. Sen et al., 2012a Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res. 22: 1558–1566.
    • (2012) Genome Res , vol.22 , pp. 1558-1566
    • King, E.G.1    Merkes, C.M.2    McNeil, C.L.3    Hoofer, S.R.4    Sen, S.5
  • 25
    • 84863880314 scopus 로고    scopus 로고
    • Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits
    • King, E. G., S. J. Macdonald, and A. D. Long, 2012b Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 191: 935–949.
    • (2012) Genetics , vol.191 , pp. 935-949
    • King, E.G.1    Macdonald, S.J.2    Long, A.D.3
  • 26
    • 68249120152 scopus 로고    scopus 로고
    • A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana
    • Kover, P. X., W. Valdar, J. Trakalo, N. Scarcelli, I. M. Ehrenreich et al., 2009 A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5(7): e1000551.
    • (2009) PLoS Genet , vol.5 , Issue.7
    • Kover, P.X.1    Valdar, W.2    Trakalo, J.3    Scarcelli, N.4    Ehrenreich, I.M.5
  • 27
    • 0024508964 scopus 로고
    • Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps
    • Lander, E. S., and D. Botstein, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199.
    • (1989) Genetics , vol.121 , pp. 185-199
    • Lander, E.S.1    Botstein, D.2
  • 28
    • 84857405495 scopus 로고    scopus 로고
    • A general Bayesian approach to analyzing diallel crosses of inbred strains
    • Lenarcic, A. B., K. L. Svenson, G. A. Churchill, and W. Valdar, 2012 A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190: 413–435.
    • (2012) Genetics , vol.190 , pp. 413-435
    • Lenarcic, A.B.1    Svenson, K.L.2    Churchill, G.A.3    Valdar, W.4
  • 29
    • 33645517140 scopus 로고    scopus 로고
    • Likelihood-based inference on haplotype effects in genetic association studies
    • Lin, D. Y., and D. Zeng, 2006 Likelihood-based inference on haplotype effects in genetic association studies. J. Am. Stat. Assoc. 101(473): 89–104.
    • (2006) J. Am. Stat. Assoc , vol.101 , Issue.473 , pp. 89-104
    • Lin, D.Y.1    Zeng, D.2
  • 30
    • 77954187717 scopus 로고    scopus 로고
    • Efficient genome ancestry inference in complex pedigrees with inbreeding
    • Liu, E. Y., Q. Zhang, L. McMillan, F. Pardo-Manuel de Villena, and W. Wang, 2010 Efficient genome ancestry inference in complex pedigrees with inbreeding. Bioinformatics 26(12): i199–i207.
    • (2010) Bioinformatics , vol.26 , Issue.12 , pp. 199-207
    • Liu, E.Y.1    Zhang, Q.2    McMillan, L.3    Pardo-Manuel De Villena, F.4    Wang, W.5
  • 31
    • 0000978881 scopus 로고    scopus 로고
    • A theoretical framework for sequential importance sampling with resampling
    • A. Doucet, N. Freitas, and N. Gordon. Springer-Verlag, New York
    • Liu, J., R. Chen, and T. Logvinenko, 2001 A theoretical framework for sequential importance sampling with resampling, pp. 225–246 in Sequential Monte Carlo Methods in Practice, edited by A. Doucet, N. Freitas, and N. Gordon. Springer-Verlag, New York.
    • (2001) Sequential Monte Carlo Methods in Practice , pp. 225-246
    • Liu, J.1    Chen, R.2    Logvinenko, T.3
  • 32
    • 84907907739 scopus 로고    scopus 로고
    • An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: Creation, properties, and validation
    • Mackay, I. J., P. Bansept-Basler, T. Barber, A. R. Bentley, J. Cockram et al., 2014 An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation. G3 (Bethesda) 4: 1603–1610.
    • (2014) G3 (Bethesda) , vol.4 , pp. 1603-1610
    • Mackay, I.J.1    Bansept-Basler, P.2    Barber, T.3    Bentley, A.R.4    Cockram, J.5
  • 33
    • 84907978425 scopus 로고    scopus 로고
    • Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation intercross population
    • Marriage, T. N., E. G. King, A. D. Long, and S. J. Macdonald, 2014 Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation intercross population. Genetics 198: 45–57.
    • (2014) Genetics , vol.198 , pp. 45-57
    • Marriage, T.N.1    King, E.G.2    Long, A.D.3    Macdonald, S.J.4
  • 36
    • 84895886695 scopus 로고    scopus 로고
    • Using the emerging Collaborative Cross to probe the immune system
    • Phillippi, J., Y. Xie, D. R. Miller, T. A. Bell, Z. Zhang et al., 2014 Using the emerging Collaborative Cross to probe the immune system. Genes Immun. 15(1): 38–46.
    • (2014) Genes Immun , vol.15 , Issue.1 , pp. 38-46
    • Phillippi, J.1    Xie, Y.2    Miller, D.R.3    Bell, T.A.4    Zhang, Z.5
  • 39
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team, R Foundation for Statistical Computing, Vienna
    • R Development Core Team, 2011 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
    • (2011) R: A Language and Environment for Statistical Computing
  • 41
    • 79958232730 scopus 로고    scopus 로고
    • Detecting major genetic loci controlling phenotypic variability in experimental crosses
    • Rönnegård, L., and W. Valdar, 2011 Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics 188: 435–447.
    • (2011) Genetics , vol.188 , pp. 435-447
    • Rönnegård, L.1    Valdar, W.2
  • 42
    • 62849120031 scopus 로고    scopus 로고
    • Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations
    • Rue, H. v., S. Martino, and N. Chopin, 2009 Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. J. R. Stat. Soc. B 71(2): 319–392.
    • (2009) J. R. Stat. Soc. B , vol.71 , Issue.2 , pp. 319-392
    • Rue, H.V.1    Martino, S.2    Chopin, N.3
  • 43
    • 0031961421 scopus 로고    scopus 로고
    • Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data
    • Sillanpaa, M. J., and E. Arjas, 1998 Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373–1388.
    • (1998) Genetics , vol.148 , pp. 1373-1388
    • Sillanpaa, M.J.1    Arjas, E.2
  • 44
    • 0032893464 scopus 로고    scopus 로고
    • Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data
    • Sillanpaa, M. J., and E. Arjas, 1999 Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605–1619.
    • (1999) Genetics , vol.151 , pp. 1605-1619
    • Sillanpaa, M.J.1    Arjas, E.2
  • 45
    • 84868566945 scopus 로고    scopus 로고
    • Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats. Physiol
    • Solberg Woods, L. C., K. L. Holl, D. Oreper, Y. Xie, S.-W. Tsaih et al., 2012 Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats. Physiol. Genomics 44(21): 1013–1026.
    • (2012) Genomics , vol.44 , Issue.21 , pp. 1013-1026
    • Solberg Woods, L.C.1    Holl, K.L.2    Oreper, D.3    Xie, Y.4    Tsaih, S.-W.5
  • 47
    • 84857410370 scopus 로고    scopus 로고
    • High-resolution genetic mapping using the mouse Diversity Outbred population
    • Svenson, K. L., D. M. Gatti, W. Valdar, C. E. Welsh, R. Cheng et al., 2012 High-resolution genetic mapping using the mouse Diversity Outbred population. Genetics 190: 437–447.
    • (2012) Genetics , vol.190 , pp. 437-447
    • Svenson, K.L.1    Gatti, D.M.2    Valdar, W.3    Welsh, C.E.4    Cheng, R.5
  • 48
    • 0032979854 scopus 로고    scopus 로고
    • High-resolution mapping of quantitative trait loci in outbred mice
    • Talbot, C. J., A. Nicod, S. S. Cherny, D. W. Fulker, C. Collins et al., 1999 High-resolution mapping of quantitative trait loci in outbred mice. Nat. Genet. 21(3): 305–308.
    • (1999) Nat. Genet , vol.21 , Issue.3 , pp. 305-308
    • Talbot, C.J.1    Nicod, A.2    Cherny, S.S.3    Fulker, D.W.4    Collins, C.5
  • 49
    • 84907982004 scopus 로고    scopus 로고
    • Identification of a Novel Gene for Diabetic Traits in Rats, Mice, and Humans
    • Tsaih, S., K. Holl, S. Jia, M. Kaldunski, M. Tschannen et al., 2014 Identification of a Novel Gene for Diabetic Traits in Rats, Mice, and Humans. Genetics 198: 17–29.
    • (2014) Genetics , vol.198 , pp. 17-29
    • Tsaih, S.1    Holl, K.2    Jia, S.3    Kaldunski, M.4    Tschannen, M.5
  • 50
    • 33746540478 scopus 로고    scopus 로고
    • Genome-wide genetic association of complex traits in heterogeneous stock mice
    • Valdar, W., L. C. Solberg, D. Gauguier, S. Burnett, P. Klenerman et al., 2006a Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat. Genet. 38: 879–887.
    • (2006) Nat. Genet , vol.38 , pp. 879-887
    • Valdar, W.1    Solberg, L.C.2    Gauguier, D.3    Burnett, S.4    Klenerman, P.5
  • 52
    • 68249130288 scopus 로고    scopus 로고
    • Mapping in structured populations by resample model averaging
    • Valdar, W., C. C. Holmes, R. Mott, and J. Flint, 2009 Mapping in structured populations by resample model averaging. Genetics 182: 1263–1277.
    • (2009) Genetics , vol.182 , pp. 1263-1277
    • Valdar, W.1    Holmes, C.C.2    Mott, R.3    Flint, J.4
  • 53
    • 75949102155 scopus 로고    scopus 로고
    • Technical note: An R package for fitting generalized linear mixed models in animal breeding
    • Vazquez, A. I., D. M. Bates, G. J. M. Rosa, D. Gianola, and K. A. Weigel, 2010 Technical note: an R package for fitting generalized linear mixed models in animal breeding. J. Anim. Sci. 88(2): 497–504.
    • (2010) J. Anim. Sci , vol.88 , Issue.2 , pp. 497-504
    • Vazquez, A.I.1    Bates, D.M.2    Rosa, G.J.M.3    Gianola, D.4    Weigel, K.A.5
  • 54
    • 31544436869 scopus 로고    scopus 로고
    • Using progenitor strain information to identify quantitative trait nucleotides in outbred mice
    • Yalcin, B., J. Flint, and R. Mott, 2005 Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. Genetics 171: 673–681.
    • (2005) Genetics , vol.171 , pp. 673-681
    • Yalcin, B.1    Flint, J.2    Mott, R.3
  • 55
    • 79955942997 scopus 로고    scopus 로고
    • Bayesian multiple quantitative trait loci mapping for recombinant inbred intercrosses
    • Yuan, Z., F. Zou, and Y. Liu, 2011 Bayesian multiple quantitative trait loci mapping for recombinant inbred intercrosses. Genetics 188: 189–195.
    • (2011) Genetics , vol.188 , pp. 189-195
    • Yuan, Z.1    Zou, F.2    Liu, Y.3
  • 56
    • 0036284203 scopus 로고    scopus 로고
    • Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals
    • Zaykin, D. V., P. H. Westfall, S. S. Young, M. a. Karnoub, M. J. Wagner et al., 2002 Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum. Hered. 53(2): 79–91.
    • (2002) Hum. Hered , vol.53 , Issue.2 , pp. 79-91
    • Zaykin, D.V.1    Westfall, P.H.2    Young, S.S.3    Karnoub, M.A.4    Wagner, M.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.