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Volumn 6, Issue 2, 2016, Pages 263-279

The mouse universal genotyping array: From substrains to subspecies

(23)  Morgan, Andrew P a,b   Fu, Chen Ping c   Kao, Chia Yu c   Welsh, Catherine E e   Didion, John P a,b   Yadgary, Liran a,b   Hyacinth, Leeanna a,b   Ferris, Martin T a,b   Bell, Timothy A a,b   Miller, Darla R a,b   Giusti Rodriguez, Paola a,b   Nonneman, Randal J a,b   Cook, Kevin D a,b   Whitmire, Jason K a,b   Gralinski, Lisa E b,d   Keller, Mark f   Attie, Alan D f   Churchill, Gary A g   Petkov, Petko g   Sullivan, Patrick F a,b   more..


Author keywords

Genetic mapping; Inbred strains; Microarrays

Indexed keywords

DNA PROBE; EXPERIMENTAL MOUSE; GENE MAPPING; GENE MUTATION; GENETIC POLYMORPHISM; GENOTYPE; MAJOR CLINICAL STUDY; MUS MUSCULUS; QUALITY CONTROL; RECOMBINANT INBRED STRAIN; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES; ALLELE; ANIMAL; BIOLOGY; CHROMOSOMAL MAPPING; DNA MICROARRAY; GENE DOSAGE; GENOME; GENOMICS; INBRED MOUSE STRAIN; MOUSE; PHYLOGENY; POPULATION GENETICS; PROCEDURES;

EID: 85014700579     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.115.022087     Document Type: Article
Times cited : (169)

References (54)
  • 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: 1213-1222.
    • (2011) Genome Res. , vol.21 , pp. 1213-1222
    • Aylor, D.L.1    Valdar, W.2    Foulds-Mathes, W.3    Buus, R.J.4    Verdugo, R.A.5
  • 2
    • 84924388025 scopus 로고    scopus 로고
    • PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination
    • Baker, C. L., S. Kajita, M. Walker, R. L. Saxl, N. Raghupathy et al., 2015 PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination. PLoS Genet. 11: e1004916.
    • (2015) PLoS Genet. , vol.11
    • Baker, C.L.1    Kajita, S.2    Walker, M.3    Saxl, R.L.4    Raghupathy, N.5
  • 5
    • 0021854913 scopus 로고
    • Most classical Mus musculus domesticus laboratory mouse strains carry a Mus musculus Y chromosome
    • Bishop, C. E., P. Boursot, B. Baron, F. Bonhomme, and D. Hatat, 1985 Most classical Mus musculus domesticus laboratory mouse strains carry a Mus musculus Y chromosome. Nature 315: 70-72.
    • (1985) Nature , vol.315 , pp. 70-72
    • Bishop, C.E.1    Boursot, P.2    Baron, B.3    Bonhomme, F.4    Hatat, D.5
  • 6
    • 63449086972 scopus 로고    scopus 로고
    • The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells
    • Cahan, P., Y. Li, M. Izumi, and T. A. Graubert, 2009 The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nat. Genet. 41: 430-437.
    • (2009) Nat. Genet. , vol.41 , pp. 430-437
    • Cahan, P.1    Li, Y.2    Izumi, M.3    Graubert, T.A.4
  • 8
    • 84906077788 scopus 로고    scopus 로고
    • Discovery and refinement of muscle weight QTLs in B6 x D2 advanced intercross mice
    • Carbonetto, P., R. Cheng, J. P. Gyekis, C. C. Parker, D. A. Blizard et al., 2014 Discovery and refinement of muscle weight QTLs in B6 x D2 advanced intercross mice. Physiol. Genomics 46: 571-582.
    • (2014) Physiol. Genomics , vol.46 , pp. 571-582
    • Carbonetto, P.1    Cheng, R.2    Gyekis, J.P.3    Parker, C.C.4    Blizard, D.A.5
  • 11
    • 84863115856 scopus 로고    scopus 로고
    • The genome architecture of the Collaborative Cross mouse genetic reference population
    • 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
  • 12
    • 84925842188 scopus 로고    scopus 로고
    • Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
    • Crowley, J. J., V. Zhabotynsky, W. Sun, S. Huang, I. K. Pakatci et al., 2015 Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat. Genet. 47: 353-360.
    • (2015) Nat. Genet. , vol.47 , pp. 353-360
    • Crowley, J.J.1    Zhabotynsky, V.2    Sun, W.3    Huang, S.4    Pakatci, I.K.5
  • 13
    • 38849101781 scopus 로고    scopus 로고
    • Significant gene content variation characterizes the genomes of inbred mouse strains
    • Cutler, G., L. A. Marshall, N. Chin, H. Baribault, and P. D. Kassner, 2007 Significant gene content variation characterizes the genomes of inbred mouse strains. Genome Res. 17: 1743-1754.
    • (2007) Genome Res. , vol.17 , pp. 1743-1754
    • Cutler, G.1    Marshall, L.A.2    Chin, N.3    Baribault, H.4    Kassner, P.D.5
  • 14
    • 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
  • 15
    • 84908068927 scopus 로고    scopus 로고
    • SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy
    • Didion, J. P., R. J. Buus, Z. Naghashfar, D. W. Threadgill, H. C. Morse et al., 2014 SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy. BMC Genomics 15: 847.
    • (2014) BMC Genomics , vol.15 , pp. 847
    • Didion, J.P.1    Buus, R.J.2    Naghashfar, Z.3    Threadgill, D.W.4    Morse, H.C.5
  • 16
    • 84924417008 scopus 로고    scopus 로고
    • A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2
    • Didion, J. P., A. P. Morgan, A. M.-F. Clayshulte, R. C. McMullan, L. Yadgary et al., 2015 A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PLoS Genet. 11: e1004850.
    • (2015) PLoS Genet. , vol.11
    • Didion, J.P.1    Morgan, A.P.2    Clayshulte, A.M.-F.3    McMullan, R.C.4    Yadgary, L.5
  • 17
    • 35649018206 scopus 로고    scopus 로고
    • Recurrent DNA copy number variation in the laboratory mouse
    • Egan, C. M., S. Sridhar, M. Wigler, and I. M. Hall, 2007 Recurrent DNA copy number variation in the laboratory mouse. Nat. Genet. 39: 1384- 1389.
    • (2007) Nat. Genet. , vol.39 , pp. 1384-1389
    • Egan, C.M.1    Sridhar, S.2    Wigler, M.3    Hall, I.M.4
  • 18
    • 84869235386 scopus 로고    scopus 로고
    • mclust Version 4 for R: Normal mixture modeling for model-based clustering, classification, and density estimation
    • Technical Report No. 597, Department of Statistics, University of Washington.
    • Fraley, C., A. E. Raftery, T. B. Murphy, and L. Scrucca, 2012 mclust Version 4 for R: normal mixture modeling for model-based clustering, classification, and density estimation.
    • (2012)
    • Fraley, C.1    Raftery, A.E.2    Murphy, T.B.3    Scrucca, L.4
  • 21
    • 84907911617 scopus 로고    scopus 로고
    • Quantitative trait locus mapping methods for Diversity Outbred mice
    • Gatti, D. M., K. L. Svenson, A. Shabalin, L.-Y. Wu, W. Valdar et al., 2014 Quantitative trait locus mapping methods for Diversity Outbred mice. G3 (Bethesda) 4: 1623-1633.
    • (2014) G3 (Bethesda , vol.4 , pp. 1623-1633
    • Gatti, D.M.1    Svenson, K.L.2    Shabalin, A.3    Wu, L.-Y.4    Valdar, W.5
  • 24
    • 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, and 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
  • 25
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., and S. L. Salzberg, 2012 Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 26
    • 84890081976 scopus 로고    scopus 로고
    • Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
    • arXiv:1303. 3997v1 [q-bio.GN].
    • Li, H., 2013 Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303. 3997v1 [q-bio.GN].
    • (2013)
    • Li, H.1
  • 27
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 30
    • 17044441930 scopus 로고    scopus 로고
    • Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse
    • Lindblad-Toh, K., E. Winchester, M. J. Daly, D. G. Wang, J. N. Hirschhorn et al., 2000 Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat. Genet. 24: 381-386.
    • (2000) Nat. Genet. , vol.24 , pp. 381-386
    • Lindblad-Toh, K.1    Winchester, E.2    Daly, M.J.3    Wang, D.G.4    Hirschhorn, J.N.5
  • 31
    • 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
  • 32
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., 2010 The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297-1303.
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5
  • 33
    • 84957951126 scopus 로고    scopus 로고
    • argyle: An R package for analysis of Illumina genotyping arrays
    • Morgan, A. P., 2015 argyle: an R package for analysis of Illumina genotyping arrays. G3 (Bethesda) 6: 281-286.
    • (2015) G3 (Bethesda , vol.6 , pp. 281-286
    • Morgan, P.A.1
  • 34
    • 84943820952 scopus 로고    scopus 로고
    • Informatics resources for the collaborative cross and related mouse populations
    • Morgan, A. P., and C. E. Welsh, 2015 Informatics resources for the collaborative cross and related mouse populations. Mamm. Genome 26: 521-539.
    • (2015) Mamm. Genome , vol.26 , pp. 521-539
    • Morgan, A.P.1    Welsh, C.E.2
  • 35
    • 0036155965 scopus 로고    scopus 로고
    • Evolution of the initiating enzymes of the complement system
    • reviews1001 1.
    • Nonaka, M. and S. Miyazawa, 2001 Evolution of the initiating enzymes of the complement system. Genome Biol. 3: reviews1001. 1.
    • (2001) Genome Biol. , vol.3
    • Nonaka, M.1    Miyazawa, S.2
  • 36
    • 33748272115 scopus 로고    scopus 로고
    • High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
    • Peiffer, D. A., J. M. Le, F. J. Steemers, W. Chang, T. Jenniges et al., 2006 High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 16: 1136-1148.
    • (2006) Genome Res. , vol.16 , pp. 1136-1148
    • Peiffer, D.A.1    Le, J.M.2    Steemers, F.J.3    Chang, W.4    Jenniges, T.5
  • 37
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R., and I. M. Hall, 2010 BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 38
    • 77951860138 scopus 로고    scopus 로고
    • Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    • Quinlan, A. R., R. A. Clark, S. Sokolova, M. L. Leibowitz, Y. Zhang et al., 2010 Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res. 20: 623- 635.
    • (2010) Genome Res. , vol.20 , pp. 623-635
    • Quinlan, A.R.1    Clark, R.A.2    Sokolova, S.3    Leibowitz, M.L.4    Zhang, Y.5
  • 39
    • 84897108137 scopus 로고    scopus 로고
    • The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis
    • Rogala, A. R., A. P. Morgan, A. M. Christensen, T. J. Gooch, T. A. Bell et al., 2014 The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. Mamm. Genome 25: 95-108.
    • (2014) Mamm. Genome , vol.25 , pp. 95-108
    • Rogala, A.R.1    Morgan, A.P.2    Christensen, A.M.3    Gooch, T.J.4    Bell, T.A.5
  • 40
    • 0003903343 scopus 로고    scopus 로고
    • Molecular Cloning: A Laboratory Manual
    • Ed. 3rd, Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY.
    • Sambrook, J., and D. W. Russell, 2006 Molecular Cloning: A Laboratory Manual, Vol. 3, Ed. 3rd. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY.
    • (2006) , vol.3
    • Sambrook, J.1    Russell, D.W.2
  • 41
  • 42
    • 33845500349 scopus 로고    scopus 로고
    • A high-resolution single nucleotide polymorphism genetic map of the mouse genome
    • Shifman, S., J. T. Bell, R. R. Copley, M. S. Taylor, R. W. Williams et al., 2006 A high-resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biol. 4: e395.
    • (2006) PLoS Biol. , vol.4
    • Shifman, S.1    Bell, J.T.2    Copley, R.R.3    Taylor, M.S.4    Williams, R.W.5
  • 43
    • 54949156063 scopus 로고    scopus 로고
    • Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
    • Staaf, J., J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist et al., 2008 Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 9: 409.
    • (2008) BMC Bioinformatics , vol.9 , pp. 409
    • Staaf, J.1    Vallon-Christersson, J.2    Lindgren, D.3    Juliusson, G.4    Rosenquist, R.5
  • 44
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis, A., 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312- 1313.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 45
    • 31344476038 scopus 로고    scopus 로고
    • Wholegenome genotyping with the single-base extension assay
    • Steemers, F. J., W. Chang, G. Lee, D. L. Barker, R. Shen et al., 2006 Wholegenome genotyping with the single-base extension assay. Nat. Methods 3: 31-33.
    • (2006) Nat. Methods , vol.3 , pp. 31-33
    • Steemers, F.J.1    Chang, W.2    Lee, G.3    Barker, D.L.4    Shen, R.5
  • 46
    • 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
  • 47
    • 0031838608 scopus 로고    scopus 로고
    • Artificial selection for increased wheel-running behavior in house mice
    • Swallow, J. G., P. A. Carter, and T. Garland, 1998 Artificial selection for increased wheel-running behavior in house mice. Behav. Genet. 28: 227- 237.
    • (1998) Behav. Genet. , vol.28 , pp. 227-237
    • Swallow, J.G.1    Carter, P.A.2    Garland, T.3
  • 48
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • The International HapMap Consortium, 2005 A haplotype map of the human genome. Nature 437: 1299-1320.
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 49
    • 35948984173 scopus 로고    scopus 로고
    • PennCNV: An integrated hidden markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    • Wang, K., M. Li, D. Hadley, R. Liu, J. Glessner et al., 2007 PennCNV: An integrated hidden markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17: 1665-1674.
    • (2007) Genome Res. , vol.17 , pp. 1665-1674
    • Wang, K.1    Li, M.2    Hadley, D.3    Liu, R.4    Glessner, J.5
  • 53
    • 69549102945 scopus 로고    scopus 로고
    • A customized and versatile high-density genotyping array for the mouse
    • Yang, H., Y. Ding, L. N. Hutchins, J. Szatkiewicz, T. a. Bell et al., 2009 A customized and versatile high-density genotyping array for the mouse. Nat. Methods 6: 663-666.
    • (2009) Nat. Methods , vol.6 , pp. 663-666
    • Yang, H.1    Ding, Y.2    Hutchins, L.N.3    Szatkiewicz, J.4    Bell, T.5
  • 54
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.