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Volumn 14, Issue , 2013, Pages

Methods of tagSNP selection and other variables affecting imputation accuracy in swine

Author keywords

Genotype imputation; Pigs; Reference panel size

Indexed keywords

ACCURACY; ARTICLE; CHROMOSOME; DENSITY; FEMALE; GENOTYPE; GENOTYPING TECHNIQUE; HAPLOTYPE; MALE; NONHUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE;

EID: 84874016729     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-14-8     Document Type: Article
Times cited : (36)

References (40)
  • 1
    • 84859042551 scopus 로고    scopus 로고
    • Design of a Bovine Low-Density SNP Array Optimized for Imputation
    • 10.1371/journal.pone.0034130, 3314603, 22470530, Van Tassell CP
    • Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S, Gietzen KJ, Hayes BJ, Lawley CT, Sonstegard TS, Van Tassell CP Design of a Bovine Low-Density SNP Array Optimized for Imputation. PLoS ONE 2012, 7(3):e34130. [http://dx.plos.org/10.1371/journal.pone.0034130], 10.1371/journal.pone.0034130, 3314603, 22470530, Van Tassell CP.
    • (2012) PLoS ONE , vol.7 , Issue.3
    • Boichard, D.1    Chung, H.2    Dassonneville, R.3    David, X.4    Eggen, A.5    Fritz, S.6    Gietzen, K.J.7    Hayes, B.J.8    Lawley, C.T.9    Sonstegard, T.S.10
  • 2
    • 67651107321 scopus 로고    scopus 로고
    • Development and Characterization of a High Density SNP Genotyping Assay for Cattle
    • , 10.1371/journal.pone.0005350, 2669730, 19390634, Tassell CPV
    • Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TPL, Sonstegard TS, Tassell CPV Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One 2009, 4(4):e5350. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005350], 10.1371/journal.pone.0005350, 2669730, 19390634, Tassell CPV.
    • (2009) PLoS One , vol.4 , Issue.4
    • Matukumalli, L.K.1    Lawley, C.T.2    Schnabel, R.D.3    Taylor, J.F.4    Allan, M.F.5    Heaton, M.P.6    O'Connell, J.7    Moore, S.S.8    Smith, T.P.L.9    Sonstegard, T.S.10
  • 3
    • 79955738465 scopus 로고    scopus 로고
    • Genomic evaluations with many more genotypes
    • 10.1186/1297-9686-43-10, 3056758, 21366914
    • VanRaden PM, O'Connell JR, Wiggans GR, Weigel KA Genomic evaluations with many more genotypes. Genet Sel Evol 2011, 43:10. [http://www.ncbi.nlm.nih.gov/pubmed/21366914], 10.1186/1297-9686-43-10, 3056758, 21366914
    • (2011) Genet Sel Evol , vol.43 , pp. 10
    • VanRaden, P.M.1    O'Connell, J.R.2    Wiggans, G.R.3    Weigel, K.A.4
  • 7
    • 59349098163 scopus 로고    scopus 로고
    • Invited review: Genomic selection in dairy cattle: Progress and challenges
    • 10.3168/jds.2008-1646, 19164653
    • Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Invited review: Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci 2009, 92(2):433-443. [http://www.ncbi.nlm.nih.gov/pubmed/19164653], 10.3168/jds.2008-1646, 19164653.
    • (2009) J Dairy Sci , vol.92 , Issue.2 , pp. 433-443
    • Hayes, B.J.1    Bowman, P.J.2    Chamberlain, A.J.3    Goddard, M.E.4
  • 8
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • 1461589, 11290733
    • Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157(4):1819-1829. [http://www.genetics.org/content/157/4/1819.abstract], 1461589, 11290733.
    • (2001) Genetics , vol.157 , Issue.4 , pp. 1819-1829
    • Meuwissen, T.H.1    Hayes, B.J.2    Goddard, M.E.3
  • 9
    • 79959332314 scopus 로고    scopus 로고
    • Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations
    • 10.3168/jds.2011-4299, 21700057
    • Dassonneville R, Brondum RF, Druet T, Fritz S, Guillaume F, Guldbrandtsen B, Lund MS, Ducrocq V, Su G. Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations. J Dairy Sci 2011, 94(7):3679-3686. [http://www.ncbi.nlm.nih.gov/pubmed/21700057], 10.3168/jds.2011-4299, 21700057.
    • (2011) J Dairy Sci , vol.94 , Issue.7 , pp. 3679-3686
    • Dassonneville, R.1    Brondum, R.F.2    Druet, T.3    Fritz, S.4    Guillaume, F.5    Guldbrandtsen, B.6    Lund, M.S.7    Ducrocq, V.8    Su, G.9
  • 10
    • 78649235216 scopus 로고    scopus 로고
    • Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle
    • 10.3168/jds.2010-3149, 20965358
    • Weigel KA, de los C, Vazquez AI, Rosa GJM, Gianola D, Tassell CPV. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. J Dairy Sci 2010, 93(11):5423-5435. [http://www.ncbi.nlm.nih.gov/pubmed/20965358], 10.3168/jds.2010-3149, 20965358.
    • (2010) J Dairy Sci , vol.93 , Issue.11 , pp. 5423-5435
    • Weigel, K.A.1    de los, C.2    Vazquez, A.I.3    Rosa, G.J.M.4    Gianola, D.5    Tassell, C.P.V.6
  • 11
    • 79960147440 scopus 로고    scopus 로고
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection
    • 10.1017/S1751731111000309, 22440168
    • Berry DP, Kearney JF. Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection. Animal 2011, 5(08):1162-1169. [http://www.ncbi.nlm.nih.gov/pubmed/22440168], 10.1017/S1751731111000309, 22440168.
    • (2011) Animal , vol.5 , Issue.8 , pp. 1162-1169
    • Berry, D.P.1    Kearney, J.F.2
  • 12
    • 67849094221 scopus 로고    scopus 로고
    • Genomic Selection Using Low-Density Marker Panels
    • 10.1534/genetics.108.100289, 2674831, 19299339
    • Habier D, Fernando RL, Dekkers JCM. Genomic Selection Using Low-Density Marker Panels. Genetics 2009, 182:343-353. [http://www.genetics.org/content/182/1/343.abstract], 10.1534/genetics.108.100289, 2674831, 19299339.
    • (2009) Genetics , vol.182 , pp. 343-353
    • Habier, D.1    Fernando, R.L.2    Dekkers, J.C.M.3
  • 13
    • 62649155943 scopus 로고    scopus 로고
    • A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals
    • 10.1016/j.ajhg.2009.01.005, 2668004, 19200528
    • Browning BL, Browning SR. A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals. Am J Hum Genet 2009, 84(2):210-223. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668004/], 10.1016/j.ajhg.2009.01.005, 2668004, 19200528.
    • (2009) Am J Hum Genet , vol.84 , Issue.2 , pp. 210-223
    • Browning, B.L.1    Browning, S.R.2
  • 14
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase
    • 10.1086/502802, 1424677, 16532393
    • Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 2006, 78(4):629-644. [http://www.ncbi.nlm.nih.gov/pubmed/16532393], 10.1086/502802, 1424677, 16532393.
    • (2006) Am J Hum Genet , vol.78 , Issue.4 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 15
    • 84856920619 scopus 로고    scopus 로고
    • Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs
    • Hickey JM, Crossa J, de los Campos G, Babu R Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs. Crop Sci 2012, 52(2):654. [https://www.agronomy.org/publications/cs/abstracts/52/2/654]
    • (2012) Crop Sci , vol.52 , Issue.2 , pp. 654
    • Hickey, J.M.1    Crossa, J.2    Babu, R.3    de los Campos, G.4
  • 16
    • 84855698387 scopus 로고    scopus 로고
    • Accuracy of genotype imputation in sheep breeds
    • Hayes BJ, Bowman PJ, Daetwyler HD, Kijas JW Accuracy of genotype imputation in sheep breeds. Anim Genet 2012, 43:72-80. [http://www.ncbi.nlm.nih.gov/pubmed/22221027]
    • (2012) Anim Genet , vol.43 , pp. 72-80
    • Hayes, B.J.1    Bowman, P.J.2    Daetwyler, H.D.3    Kijas, J.W.4
  • 17
    • 33947124162 scopus 로고    scopus 로고
    • Informative SNP selection methods based on SNP prediction
    • He J, Zelikovsky A. Informative SNP selection methods based on SNP prediction. IEEE Trans Nanobioscience 2007, 6:60-67. [http://www.ncbi.nlm.nih.gov/pubmed/17393851].
    • (2007) IEEE Trans Nanobioscience , vol.6 , pp. 60-67
    • He, J.1    Zelikovsky, A.2
  • 18
    • 32144431911 scopus 로고    scopus 로고
    • An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
    • Qin ZS, Gopalakrishnan S, Abecasis GR. An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. Bioinf 2006, 22(2):220-225. [http://www.ncbi.nlm.nih.gov/pubmed/16269414].
    • (2006) Bioinf , vol.22 , Issue.2 , pp. 220-225
    • Qin, Z.S.1    Gopalakrishnan, S.2    Abecasis, G.R.3
  • 19
    • 33749818757 scopus 로고    scopus 로고
    • MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression
    • He J, Zelikovsky A. MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression. Bioinf 2006, 22(20):2558-2561. [http://bioinformatics.oxfordjournals.org/content/22/20/2558.full].
    • (2006) Bioinf , vol.22 , Issue.20 , pp. 2558-2561
    • He, J.1    Zelikovsky, A.2
  • 20
    • 84863845193 scopus 로고    scopus 로고
    • Genotype Imputation with Thousands of Genomes
    • Howie B, Marchini J. Genotype Imputation with Thousands of Genomes. G3 2011, 1(457):13. [http://www.g3journal.org/content/1/6/457.full].
    • (2011) G3 , vol.1 , Issue.457 , pp. 13
    • Howie, B.1    Marchini, J.2
  • 21
    • 62649089065 scopus 로고    scopus 로고
    • Genotype-imputation accuracy across worldwide human populations
    • 10.1016/j.ajhg.2009.01.013, 2668016, 19215730
    • Huang L, Li Y, Singleton AB, Hardy JA, Abecasis G, Rosenberg NA, Scheet P. Genotype-imputation accuracy across worldwide human populations. Am J Hum Genet 2009, 84(2):235-250. [http://www.ncbi.nlm.nih.gov/pubmed/19215730], 10.1016/j.ajhg.2009.01.013, 2668016, 19215730.
    • (2009) Am J Hum Genet , vol.84 , Issue.2 , pp. 235-250
    • Huang, L.1    Li, Y.2    Singleton, A.B.3    Hardy, J.A.4    Abecasis, G.5    Rosenberg, N.A.6    Scheet, P.7
  • 23
    • 84855798536 scopus 로고    scopus 로고
    • Estimation of linkage disequilibrium in four US pig breeds
    • 10.1186/1471-2164-13-24, 3269977, 22252454
    • Badke YM, Bates RO, Ernst CW, Schwab C, Steibel JP. Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics 2012, 13:24. [http://www.biomedcentral.com/1471-2164/13/24], 10.1186/1471-2164-13-24, 3269977, 22252454.
    • (2012) BMC Genomics , vol.13 , pp. 24
    • Badke, Y.M.1    Bates, R.O.2    Ernst, C.W.3    Schwab, C.4    Steibel, J.P.5
  • 24
    • 71549118527 scopus 로고    scopus 로고
    • Reliability of genomic predictions across multiple populations
    • 10.1534/genetics.109.104935, 2787438, 19822733
    • de Roos A, Hayes BJ, Goddard ME. Reliability of genomic predictions across multiple populations. Genetics 2009, 183(4):1545-1553. [http://www.genetics.org/content/183/4/1545.abstract], 10.1534/genetics.109.104935, 2787438, 19822733.
    • (2009) Genetics , vol.183 , Issue.4 , pp. 1545-1553
    • de Roos, A.1    Hayes, B.J.2    Goddard, M.E.3
  • 25
    • 84892672480 scopus 로고    scopus 로고
    • Documentation of BEAGLE 3.3.1
    • Browning BL. Documentation of BEAGLE 3.3.1. [http://faculty.washington.edu/browning/beagle/beagle.html].
    • Browning, B.L.1
  • 26
    • 78751490178 scopus 로고    scopus 로고
    • A comparison of approaches to account for uncertainty in analysis of imputed genotypes
    • 10.1002/gepi.20552, 3143715, 21254217
    • Zheng J, Li Y, Abecasis GR, Scheet P. A comparison of approaches to account for uncertainty in analysis of imputed genotypes. Genet Epidemiol 2011, 35(2):102-110. [http://www.ncbi.nlm.nih.gov/pubmed/21254217], 10.1002/gepi.20552, 3143715, 21254217.
    • (2011) Genet Epidemiol , vol.35 , Issue.2 , pp. 102-110
    • Zheng, J.1    Li, Y.2    Abecasis, G.R.3    Scheet, P.4
  • 28
    • 84859051417 scopus 로고    scopus 로고
    • Short communication: Imputation performances of 3 low-density marker panels in beef and dairy cattle
    • 10.3168/jds.2011-5133, 22720970
    • Dassonneville R, Fritz S, Ducrocq V, Boichard D. Short communication: Imputation performances of 3 low-density marker panels in beef and dairy cattle. Journal of dairy science 2012, 95(7):4136-40. [http://www.ncbi.nlm.nih.gov/pubmed/22720970], 10.3168/jds.2011-5133, 22720970.
    • (2012) Journal of dairy science , vol.95 , Issue.7 , pp. 4136-4140
    • Dassonneville, R.1    Fritz, S.2    Ducrocq, V.3    Boichard, D.4
  • 29
    • 4243709036 scopus 로고
    • Local regression models
    • Pacific Grove: Wadsworth & Brooks/Cole, Chambers JM, Hastie TJ
    • Cleveland WS, Grosse E, Shyu WM. Local regression models. 1992, 309-376. Pacific Grove: Wadsworth & Brooks/Cole, Chambers JM, Hastie TJ.
    • (1992) , pp. 309-376
    • Cleveland, W.S.1    Grosse, E.2    Shyu, W.M.3
  • 30
    • 70449482138 scopus 로고    scopus 로고
    • Assessment of the swine protein-annotated oligonucleotide microarray
    • 10.1111/j.1365-2052.2009.01928.x, 19515086
    • Steibel J, Wysocki M, Lunney J. Assessment of the swine protein-annotated oligonucleotide microarray. Anim Genet 2009, 40(6):883-893. http://www.ncbi.nlm.nih.gov/pubmed/19515086], 10.1111/j.1365-2052.2009.01928.x, 19515086.
    • (2009) Anim Genet , vol.40 , Issue.6 , pp. 883-893
    • Steibel, J.1    Wysocki, M.2    Lunney, J.3
  • 31
    • 0036338150 scopus 로고    scopus 로고
    • Merlin-rapid analysis of dense genetic maps using sparse gene flow trees
    • 10.1038/ng786, 11731797
    • Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002, 30:97-101. [http://www.ncbi.nlm.nih.gov/pubmed/11731797], 10.1038/ng786, 11731797.
    • (2002) Nat Genet , vol.30 , pp. 97-101
    • Abecasis, G.R.1    Cherny, S.S.2    Cookson, W.O.3    Cardon, L.R.4
  • 32
    • 79960051527 scopus 로고    scopus 로고
    • A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes
    • Hickey JM, Kinghorn BP, Tier B, Wilson JF, Dunstan N, Van Der Werf JH. A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. Genet Sel Evol GSE 2011, 43:12. [http://www.ncbi.nlm.nih.gov/pubmed/21388557].
    • (2011) Genet Sel Evol GSE , vol.43 , pp. 12
    • Hickey, J.M.1    Kinghorn, B.P.2    Tier, B.3    Wilson, J.F.4    Dunstan, N.5    Van Der Werf, J.H.6
  • 33
    • 77952054021 scopus 로고    scopus 로고
    • Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms
    • 10.3168/jds.2009-2849, 20412938
    • Weigel KA, Tassell CPV, O'Connell JR, VanRaden PM, Wiggans GR. Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. J Dairy Sci 2010, 93(5):2229-2238. [http://www.ncbi.nlm.nih.gov/pubmed/20412938], 10.3168/jds.2009-2849, 20412938.
    • (2010) J Dairy Sci , vol.93 , Issue.5 , pp. 2229-2238
    • Weigel, K.A.1    Tassell, C.P.V.2    O'Connell, J.R.3    VanRaden, P.M.4    Wiggans, G.R.5
  • 35
    • 84881546450 scopus 로고    scopus 로고
    • Genotype imputation accuracy in an F2 pig cross using high density and low density SNP panels [abstract]
    • Phoenix
    • Gualdron Duarte JL, Bates RO, Ernst CW, Raney NE, Cantet RJC, Steibel JP. Genotype imputation accuracy in an F2 pig cross using high density and low density SNP panels [abstract]. 2012, W76-W76. Phoenix.
    • (2012)
    • Gualdron Duarte, J.L.1    Bates, R.O.2    Ernst, C.W.3    Raney, N.E.4    Cantet, R.J.C.5    Steibel, J.P.6
  • 36
    • 84864376178 scopus 로고    scopus 로고
    • Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost
    • 10.1186/1297-9686-44-25, 3436735, 22849718
    • Huang Y, Hickey JM, Cleveland MA, Maltecca C. Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost. Genet, Sel, Evol : GSE 2012, 44:25. [http://www.gsejournal.org/content/44/1/25], 10.1186/1297-9686-44-25, 3436735, 22849718.
    • (2012) Genet, Sel, Evol : GSE , vol.44 , pp. 25
    • Huang, Y.1    Hickey, J.M.2    Cleveland, M.A.3    Maltecca, C.4
  • 37
    • 80053019891 scopus 로고    scopus 로고
    • Haplotype phasing: existing methods and new developments
    • 10.1038/nrg3054, 3217888, 21921926
    • Browning SR, Browning BL. Haplotype phasing: existing methods and new developments. Nat Rev Genet 2011, 12(10):703-714. [http://www.ncbi.nlm.nih.gov/pubmed/21921926], 10.1038/nrg3054, 3217888, 21921926.
    • (2011) Nat Rev Genet , vol.12 , Issue.10 , pp. 703-714
    • Browning, S.R.1    Browning, B.L.2
  • 38
    • 77951110862 scopus 로고    scopus 로고
    • Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation
    • 10.2527/jas.2009-2537, 20190174
    • Welsh CS, Stewart TS, Schwab C, Blackburn HD. Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation. J Anim Sci 2010, 88(5):1610-1618. [http://www.ncbi.nlm.nih.gov/pubmed/20190174], 10.2527/jas.2009-2537, 20190174.
    • (2010) J Anim Sci , vol.88 , Issue.5 , pp. 1610-1618
    • Welsh, C.S.1    Stewart, T.S.2    Schwab, C.3    Blackburn, H.D.4
  • 39
    • 78649359717 scopus 로고    scopus 로고
    • Marker imputation with low-density marker panels in Dutch Holstein cattle
    • 10.3168/jds.2010-3501, 20965364
    • Zhang Z, Druet T. Marker imputation with low-density marker panels in Dutch Holstein cattle. J Dairy Sci 2010, 93(11):5487-5494. [http://www.ncbi.nlm.nih.gov/pubmed/20965364], 10.3168/jds.2010-3501, 20965364.
    • (2010) J Dairy Sci , vol.93 , Issue.11 , pp. 5487-5494
    • Zhang, Z.1    Druet, T.2
  • 40
    • 84857254999 scopus 로고    scopus 로고
    • Use of the Illumina Bovine3K BeadChip in dairy genomic evaluation
    • 10.3168/jds.2011-4985, 22365235
    • Wiggans GR, Cooper TA, VanRaden PM, Olson KM, Tooker ME. Use of the Illumina Bovine3K BeadChip in dairy genomic evaluation. J Dairy Sci 2012, 95(3):1552-1558. [http://www.ncbi.nlm.nih.gov/pubmed/22365235], 10.3168/jds.2011-4985, 22365235.
    • (2012) J Dairy Sci , vol.95 , Issue.3 , pp. 1552-1558
    • Wiggans, G.R.1    Cooper, T.A.2    VanRaden, P.M.3    Olson, K.M.4    Tooker, M.E.5


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