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Volumn 4, Issue 9, 2014, Pages 1623-1633

Quantitative trait locus mapping methods for diversity outbred mice

Author keywords

Advanced; Diversity outbred; Generation; Haplotype reconstruction; Inter Cross (MAGIC); MPP; Multiparent; Multiparental populations; Quantitative trait locus mapping

Indexed keywords

ALLELE; ANIMAL EXPERIMENT; ARTICLE; BREEDING; CONTROLLED STUDY; FEMALE; GENETIC STABILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HETEROZYGOTE; HOMOZYGOTE; MALE; MATING; MOUSE; NONHUMAN; OUTBRED MOUSE STRAIN; PHENOTYPE; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; CYTOLOGY; GENETICS; LEUKOCYTE COUNT; NEUTROPHIL; OUTBRED STRAIN; PROCEDURES; QUANTITATIVE TRAIT LOCUS;

EID: 84907911617     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.013748     Document Type: Article
Times cited : (165)

References (48)
  • 1
    • 84879692177 scopus 로고    scopus 로고
    • Combined sequence-based and genetic mapping analysis of complex traits in outbred rats
    • 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.
    • (2013) Nat. Genet , vol.45 , pp. 767-775
    • Baud, A.1    Hermsen, R.2    Guryev, V.3    Stridh, P.4    Graham, D.5
  • 2
    • 0000353178 scopus 로고
    • A maximization technique occuring in the statistical analysis of probabilistic functions of Markov chains
    • Baum, L. E., Petrie, T., Soules, G., and Weiss, N., 1970 A maximization technique occuring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat. 41: 164-171.
    • (1970) Ann. Math. Stat , vol.41 , pp. 164-171
    • Baum, L.E.1    Petrie, T.2    Soules, G.3    Weiss, N.4
  • 3
    • 78650111988 scopus 로고    scopus 로고
    • Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping
    • Billings, T., E. E. Sargent, J. P. Szatkiewicz, N. Leahy, I. Y. Kwak et al., 2010 Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping. PLoS ONE 5: e15340.
    • (2010) PLoS ONE , vol.5 , pp. e15340
    • Billings, T.1    Sargent, E.E.2    Szatkiewicz, J.P.3    Leahy, N.4    Kwak, I.Y.5
  • 4
    • 84857388664 scopus 로고    scopus 로고
    • Haplotype probabilities in advanced intercross populations
    • Broman, K. W., 2012 Haplotype probabilities in advanced intercross populations. G3 Genes Genomes Genet. 2: 199-202.
    • (2012) G3 Genes Genomes Genet , vol.2 , pp. 199-202
    • Broman, K.W.1
  • 6
    • 84872040426 scopus 로고    scopus 로고
    • Chapter11 genome-wide association studies
    • Bush, W. S., and J. H. Moore, 2012 Chapter 11: genome-wide association studies. PLOS Comput. Biol. 8: e1002822.
    • (2012) PLOS Comput. Biol , vol.8 , pp. e1002822
    • Bush, W.S.1    Moore, J.H.2
  • 7
    • 84876433851 scopus 로고    scopus 로고
    • A simulation study of permutation, bootstrap, and gene dropping for assessing statistical significance in the case of unequal relatedness
    • Cheng, R., and A. A. Palmer, 2013 A simulation study of permutation, bootstrap, and gene dropping for assessing statistical significance in the case of unequal relatedness. Genetics 193: 1015-1018.
    • (2013) Genetics , vol.193 , pp. 1015-1018
    • Cheng, R.1    Palmer, A.A.2
  • 8
    • 77957157030 scopus 로고    scopus 로고
    • Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations
    • Cheng, R., J. E. Lim, K. E. Samocha, G. Sokoloff, M. Abney et al., 2010 Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations. Genetics 185: 1033-1044.
    • (2010) Genetics , vol.185 , pp. 1033-1044
    • Cheng, R.1    Lim, J.E.2    Samocha, K.E.3    Sokoloff, G.4    Abney, M.5
  • 9
    • 79960693332 scopus 로고    scopus 로고
    • QTLRel: an R package for genome-wide association studies in which relatedness is a concern
    • Cheng, R., M. Abney, A. A. Palmer, and A. D. Skol, 2011 QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet. 12: 66.
    • (2011) BMC Genet , vol.12 , pp. 66
    • Cheng, R.1    Abney, M.2    Palmer, A.A.3    Skol, A.D.4
  • 10
    • 84885770388 scopus 로고    scopus 로고
    • Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies
    • Cheng, R., C. C. Parker, M. Abney, and A. A. Palmer, 2013 Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies. G3 3: 1861-1867.
    • (2013) G3 , vol.3 , pp. 1861-1867
    • Cheng, R.1    Parker, C.C.2    Abney, M.3    Palmer, A.A.4
  • 11
    • 0024557590 scopus 로고
    • Stochastic models for heterogeneous DNA sequences
    • Churchill, G. A., 1989 Stochastic models for heterogeneous DNA sequences. Bull. Math. Biol. 51: 79-94.
    • (1989) Bull. Math. Biol , vol.51 , pp. 79-94
    • Churchill, G.A.1
  • 12
    • 0028151261 scopus 로고
    • Empirical threshold values for quantitative trait mapping
    • Churchill, G. A., and R. W. Doerge, 1994 Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
    • (1994) Genetics , vol.138 , pp. 963-971
    • Churchill, G.A.1    Doerge, R.W.2
  • 13
    • 40849100588 scopus 로고    scopus 로고
    • Naive application of permutation testing leads to inflated type I error rates
    • Churchill, G. A., and R. W. Doerge, 2008 Naive application of permutation testing leads to inflated type I error rates. Genetics 178: 609-610.
    • (2008) Genetics , vol.178 , pp. 609-610
    • Churchill, G.A.1    Doerge, R.W.2
  • 14
    • 14644441018 scopus 로고    scopus 로고
    • The Collaborative Cross, a community resource for the genetic analysis of complex traits
    • Churchill, G. A., D. C. Airey, H. Allayee, J. M. Angel, A. D. Attie et al., 2004 The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat. Genet. 36: 1133-1137.
    • (2004) Nat. Genet , vol.36 , pp. 1133-1137
    • Churchill, G.A.1    Airey, D.C.2    Allayee, H.3    Angel, J.M.4    Attie, A.D.5
  • 16
    • 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
  • 18
    • 84855886780 scopus 로고    scopus 로고
    • Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
    • Didion, J. P., H. Yang, K. Sheppard, C. P. Fu, L. McMillan et al., 2012 Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics 13: 34.
    • (2012) BMC Genomics , vol.13 , pp. 34
    • Didion, J.P.1    Yang, H.2    Sheppard, K.3    Fu, C.P.4    McMillan, L.5
  • 19
    • 66549108083 scopus 로고    scopus 로고
    • CXCR4 is a key regulator of neutrophil release from the bone marrow under basal and stress granulopoiesis conditions
    • Eash, K. J., J. M. Means, D. W. White, and D. C. Link, 2009 CXCR4 is a key regulator of neutrophil release from the bone marrow under basal and stress granulopoiesis conditions. Blood 113: 4711-4719.
    • (2009) Blood , vol.113 , pp. 4711-4719
    • Eash, K.J.1    Means, J.M.2    White, D.W.3    Link, D.C.4
  • 20
    • 15944376562 scopus 로고    scopus 로고
    • Strategies for mapping and cloning quantitative trait genes in rodents
    • Flint, J.,W. Valdar, S. Shifman, and R. Mott, 2005 Strategies for mapping and cloning quantitative trait genes in rodents. Nat. Rev. Genet. 6: 271-286.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 271-286
    • Flint, J.1    Valdar, W.2    Shifman, S.3    Mott, R.4
  • 22
    • 84869392652 scopus 로고    scopus 로고
    • Inferring ancestry in admixed populations using microaray probe intensities
    • Association for Computing Machinery, Orlando, FL
    • Fu, C., C. E. Welsh, F. Pardo-Manuel de Villena, and L. McMillan, 2012 Inferring ancestry in admixed populations using microaray probe intensities, pp. in ACM-BCB 2012. Association for Computing Machinery, Orlando, FL.
    • (2012) ACM-BCB 2012
    • Fu, C.1    Welsh, C.E.2    de Villena, P.-M.3    McMillan, L.4
  • 23
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: open software development for computational biology and bioinformatics
    • R80
    • Gentleman, R. C., V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling et al., 2004 Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5: R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5
  • 24
    • 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: 315-324.
    • (1992) Heredity , vol.69 , pp. 315-324
    • Haley, C.S.1    Knott, S.A.2
  • 25
    • 0027970508 scopus 로고
    • Further studies on the relationship between dopamine cell density and haloperidolinduced catalepsy
    • Hitzemann, B., K. Dains, S. Kanes, and R. Hitzemann, 1994 Further studies on the relationship between dopamine cell density and haloperidolinduced catalepsy. J. Pharmacol. Exp. Ther. 271: 969-976.
    • (1994) J. Pharmacol. Exp. Ther , vol.271 , pp. 969-976
    • Hitzemann, B.1    Dains, K.2    Kanes, S.3    Hitzemann, R.4
  • 26
    • 77957894341 scopus 로고    scopus 로고
    • Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse
    • Iancu, O. D., P. Darakjian, N. A. Walter, B. Malmanger, D. Oberbeck et al., 2010 Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. BMC Genomics 11: 585.
    • (2010) BMC Genomics , vol.11 , pp. 585
    • Iancu, O.D.1    Darakjian, P.2    Walter, N.A.3    Malmanger, B.4    Oberbeck, D.5
  • 27
    • 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
  • 28
    • 80052851950 scopus 로고    scopus 로고
    • Mouse genomic variation and its effect on phenotypes and gene regulation
    • Keane, T. M., L. Goodstadt, P. Danecek, M. A. White, K. Wong et al., 2011 Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-294.
    • (2011) Nature , vol.477 , pp. 289-294
    • Keane, T.M.1    Goodstadt, L.2    Danecek, P.3    White, M.A.4    Wong, K.5
  • 29
    • 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., 2012 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
  • 30
    • 68249120152 scopus 로고    scopus 로고
    • A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana
    • e1000551
    • 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: e1000551.
    • (2009) PLoS Genet , vol.5
    • Kover, P.X.1    Valdar, W.2    Trakalo, J.3    Scarcelli, N.4    Ehrenreich, I.M.5
  • 31
    • 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
  • 32
    • 0021705835 scopus 로고
    • Alcohol preference and voluntary alcohol intakes of inbred rat strains and the National Institutes of Health heterogeneous stock of rats
    • Li, T. K., and L. Lumeng, 1984 Alcohol preference and voluntary alcohol intakes of inbred rat strains and the National Institutes of Health heterogeneous stock of rats. Alcohol. Clin. Exp. Res. 8: 485-486.
    • (1984) Alcohol. Clin. Exp. Res , vol.8 , pp. 485-486
    • Li, T.K.1    Lumeng, L.2
  • 33
    • 84901303111 scopus 로고    scopus 로고
    • High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline
    • Liu, E. Y., A. P. Morgan, E. J. Chesler, W. Wang, G. A. Churchill et al., 2014 High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline. Genetics 197: 91-106.
    • (2014) Genetics , vol.197 , pp. 91-106
    • Liu, E.Y.1    Morgan, A.P.2    Chesler, E.J.3    Wang, W.4    Churchill, G.A.5
  • 34
  • 35
    • 76749151934 scopus 로고    scopus 로고
    • Prdm9 controls activation of mammalian recombination hotspots
    • Parvanov, E. D., P. M. Petkov, and K. Paigen, 2010 Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835.
    • (2010) Science , pp. 327-835
    • Parvanov, E.D.1    Petkov, P.M.2    Paigen, K.3
  • 37
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner, L. R., 1989 A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77: 257-286.
    • (1989) Proc. IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 38
    • 0034817026 scopus 로고    scopus 로고
    • A statistical framework for quantitative trait mapping
    • Sen, S., and G. A. Churchill, 2001 A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
    • (2001) Genetics , vol.159 , pp. 371-387
    • Sen, S.1    Churchill, G.A.2
  • 39
    • 84861153094 scopus 로고    scopus 로고
    • Matrix eQTL: ultra fast eQTL analysis via large matrix operations
    • Shabalin, A. A., 2012 Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28: 1353-1358.
    • (2012) Bioinformatics , vol.28 , pp. 1353-1358
    • Shabalin, A.A.1
  • 40
    • 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
  • 42
    • 40849097776 scopus 로고    scopus 로고
    • Heritability in the genomics era-concepts and misconceptions
    • Visscher, P. M., W. G. Hill, and N. R. Wray, 2008 Heritability in the genomics era-concepts and misconceptions. Nat. Rev. Genet. 9: 255- 266.
    • (2008) Nat. Rev. Genet , vol.9 , pp. 255-266
    • Visscher, P.M.1    Hill, W.G.2    Wray, N.R.3
  • 43
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
    • Viterbi, A. J., 1967 Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inf. Theory 13: 260- 269.
    • (1967) IEEE Trans. Inf. Theory , vol.13 , pp. 260-269
    • Viterbi, A.J.1
  • 45
    • 79959735506 scopus 로고    scopus 로고
    • Subspecific origin and haplotype diversity in the laboratory mouse
    • Yang, H., J. R. Wang, J. P. Didion, R. J. Buus, T. A. Bell et al., 2011 Subspecific origin and haplotype diversity in the laboratory mouse. Nat. Genet. 43: 648-655.
    • (2011) Nat. Genet , vol.43 , pp. 648-655
    • Yang, H.1    Wang, J.R.2    Didion, J.P.3    Buus, R.J.4    Bell, T.A.5
  • 46
    • 84895801913 scopus 로고    scopus 로고
    • Advantages and pitfalls in the application of mixed-model association methods
    • Yang, J., N. A. Zaitlen, M. E. Goddard, P. M. Visscher, and A. L. Price, 2014 Advantages and pitfalls in the application of mixed-model association methods. Nat. Genet. 46: 100-106.
    • (2014) Nat. Genet , vol.46 , pp. 100-106
    • Yang, J.1    Zaitlen, N.A.2    Goddard, M.E.3    Visscher, P.M.4    Price, A.L.5
  • 47
    • 84907912911 scopus 로고    scopus 로고
    • Bayesian modeling of haplotype effects in multiparent populations
    • Zhaojun, Z., W. Wang, and W. Valdar, 2014 Bayesian modeling of haplotype effects in multiparent populations. Genetics 139-156.
    • (2014) Genetics , pp. 139-156
    • Zhaojun, Z.1    Wang, W.2    Valdar, W.3
  • 48
    • 84863003734 scopus 로고    scopus 로고
    • Genome-wide efficient mixed-model analysis for association studies
    • Zhou, X., and M. Stephens, 2012 Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44: 821-824.
    • (2012) Nat. Genet , vol.44 , pp. 821-824
    • Zhou, X.1    Stephens, M.2


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