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Volumn 16, Issue 1, 2015, Pages

Impact of genetic similarity on imputation accuracy

Author keywords

F_ST; Genetic similarity; Genotype imputation; G_ST; Imputation quality; Reference panel; SNP data

Indexed keywords

ACCURACY; AFRICAN AMERICAN; ARTICLE; CAUCASIAN; COMPUTER PROGRAM; EAST ASIAN; ETHNIC DIFFERENCE; EUROPEAN; GENETIC ASSOCIATION; GENETIC DISTANCE; GENETIC PROCEDURES; GENETIC SELECTION; GENETIC SIMILARITY; GENOTYPE; GENOTYPE IMPUTATION; HUMAN; INTERMETHOD COMPARISON; MEXICAN; POPULATION GENETICS; PREDICTIVE VALIDITY; REFERENCE VALUE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH ASIAN; STATISTICAL ANALYSIS; ALGORITHM; BIOLOGICAL MODEL; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; INFORMATION PROCESSING; MOLECULAR EVOLUTION; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

EID: 84937231051     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/s12863-015-0248-2     Document Type: Article
Times cited : (23)

References (47)
  • 1
    • 42349106044 scopus 로고    scopus 로고
    • Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes
    • Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, et al. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008;40:638-45.
    • (2008) Nat Genet , vol.40 , pp. 638-645
    • Zeggini, E.1    Scott, L.J.2    Saxena, R.3    Voight, B.F.4    Marchini, J.L.5    Hu, T.6
  • 2
    • 34347357576 scopus 로고    scopus 로고
    • Conjuring SNPs to detect associations
    • Clark AG, Li J. Conjuring SNPs to detect associations. Nat Genet. 2007;39:815-6.
    • (2007) Nat Genet , vol.39 , pp. 815-816
    • Clark, A.G.1    Li, J.2
  • 3
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56-65.
    • (2012) Nature , vol.491 , pp. 56-65
    • Abecasis, G.R.1    Auton, A.2    Brooks, L.D.3    DePristo, M.A.4    Durbin, R.M.5
  • 4
    • 84930868547 scopus 로고    scopus 로고
    • Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs
    • Pistis G, Porcu E, Vrieze SI, Sidore C, Steri M, Danjou F, et al. Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs. Eur J Hum Genet. 2014;23(7):975-83.
    • (2014) Eur J Hum Genet , vol.23 , Issue.7 , pp. 975-983
    • Pistis, G.1    Porcu, E.2    Vrieze, S.I.3    Sidore, C.4    Steri, M.5    Danjou, F.6
  • 5
    • 84920943901 scopus 로고    scopus 로고
    • Tailored Selection of Study Individuals to be Sequenced in Order to Improve the Accuracy of Genotype Imputation: Choosing Individuals for Sequencing to Impute
    • Peil B, Kabisch M, Fischer C, Hamann U, Bermejo JL. Tailored Selection of Study Individuals to be Sequenced in Order to Improve the Accuracy of Genotype Imputation: Choosing Individuals for Sequencing to Impute. Genet Epidemiol. 2015;39:114-21.
    • (2015) Genet Epidemiol , vol.39 , pp. 114-121
    • Peil, B.1    Kabisch, M.2    Fischer, C.3    Hamann, U.4    Bermejo, J.L.5
  • 6
    • 34347344976 scopus 로고    scopus 로고
    • A new multipoint method for genome-wide association studies by imputation of genotypes
    • Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39:906-13.
    • (2007) Nat Genet , vol.39 , pp. 906-913
    • Marchini, J.1    Howie, B.2    Myers, S.3    McVean, G.4    Donnelly, P.5
  • 7
    • 84871083616 scopus 로고    scopus 로고
    • MaCH-Admix: Genotype Imputation for Admixed Populations: MaCH-Admix: Imputation for Admixed Populations
    • Liu EY, Li M, Wang W, Li Y. MaCH-Admix: Genotype Imputation for Admixed Populations: MaCH-Admix: Imputation for Admixed Populations. Genet Epidemiol. 2013;37:25-37.
    • (2013) Genet Epidemiol , vol.37 , pp. 25-37
    • Liu, E.Y.1    Li, M.2    Wang, W.3    Li, Y.4
  • 8
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol. 2010;34:816-34.
    • (2010) Genet Epidemiol , vol.34 , pp. 816-834
    • Li, Y.1    Willer, C.J.2    Ding, J.3    Scheet, P.4    Abecasis, G.R.5
  • 10
    • 20944448714 scopus 로고
    • Genetical Structure of Populations
    • Wright S. Genetical Structure of Populations. Nature. 1950;166:247-9.
    • (1950) Nature , vol.166 , pp. 247-249
    • Wright, S.1
  • 11
    • 0021566877 scopus 로고
    • Estimating F-Statistics for the Analysis of Population Structure
    • Weir BS, Cockerham CC. Estimating F-Statistics for the Analysis of Population Structure. Soc Study Evol. 1984;38:1358-70.
    • (1984) Soc Study Evol , vol.38 , pp. 1358-1370
    • Weir, B.S.1    Cockerham, C.C.2
  • 12
    • 0000862605 scopus 로고
    • The Interpretation of Population Structure by F-Statistics with Special Regard to Systems of Mating
    • Wright S. The Interpretation of Population Structure by F-Statistics with Special Regard to Systems of Mating. Evolution. 1965;19:395.
    • (1965) Evolution , vol.19 , pp. 395
    • Wright, S.1
  • 13
    • 0000762002 scopus 로고
    • Definition and estimation of fixation indices
    • Nei M. Definition and estimation of fixation indices. Evolution. 1986;40:643-5.
    • (1986) Evolution , vol.40 , pp. 643-645
    • Nei, M.1
  • 14
    • 0020954623 scopus 로고
    • Estimation of fixation indices and gene diversities
    • Nei M, Chesser RK. Estimation of fixation indices and gene diversities. Ann Hum Genet. 1983;47:253-9.
    • (1983) Ann Hum Genet , vol.47 , pp. 253-259
    • Nei, M.1    Chesser, R.K.2
  • 15
    • 67349176068 scopus 로고    scopus 로고
    • Genetics in geographically structured populations: defining, estimating and interpreting FST
    • Holsinger KE, Weir BS. Genetics in geographically structured populations: defining, estimating and interpreting FST. Nat Rev Genet. 2009;10:639-50.
    • (2009) Nat Rev Genet , vol.10 , pp. 639-650
    • Holsinger, K.E.1    Weir, B.S.2
  • 16
    • 84883685094 scopus 로고    scopus 로고
    • Estimating and interpreting FST: The impact of rare variants
    • Bhatia G, Patterson N, Sankararaman S, Price AL. Estimating and interpreting FST: The impact of rare variants. Genome Res. 2013;23:1514-21.
    • (2013) Genome Res , vol.23 , pp. 1514-1521
    • Bhatia, G.1    Patterson, N.2    Sankararaman, S.3    Price, A.L.4
  • 18
    • 0026709389 scopus 로고
    • Estimation of levels of gene flow from DNA sequence data
    • Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992;132:583-9.
    • (1992) Genetics , vol.132 , pp. 583-589
    • Hudson, R.R.1    Slatkin, M.2    Maddison, W.P.3
  • 19
    • 0004275709 scopus 로고
    • Molecular Evolutionary Genetics
    • New York: Columbia University Press
    • Nei M. Molecular Evolutionary Genetics. New York: Columbia University Press; 1987.
    • (1987)
    • Nei, M.1
  • 22
    • 50949096560 scopus 로고    scopus 로고
    • The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research
    • Nelson MR, Bryc K, King KS, Indap A, Boyko AR, Novembre J, et al. The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research. Am J Hum Genet. 2008;83:347-58.
    • (2008) Am J Hum Genet , vol.83 , pp. 347-358
    • Nelson, M.R.1    Bryc, K.2    King, K.S.3    Indap, A.4    Boyko, A.R.5    Novembre, J.6
  • 23
    • 85019177255 scopus 로고    scopus 로고
    • POPRES: Population Reference Sample
    • POPRES: Population Reference Sample [ http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/collection.cgi?study_id=phs000145.v2.p2 ]
  • 24
    • 77956331627 scopus 로고    scopus 로고
    • Integrating common and rare genetic variation in diverse human populations
    • International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, et al. Integrating common and rare genetic variation in diverse human populations. Nature. 2010;467:52-8.
    • (2010) Nature , vol.467 , pp. 52-58
    • Altshuler, D.M.1    Gibbs, R.A.2    Peltonen, L.3    Altshuler, D.M.4    Gibbs, R.A.5
  • 25
    • 84904613205 scopus 로고    scopus 로고
    • Homepage of Imputation software MaCH1.0.
    • Abecasis GR. Homepage of Imputation software MaCH1.0. 2014.
    • (2014)
    • Abecasis, G.R.1
  • 26
    • 84904635954 scopus 로고    scopus 로고
    • Homepage of IMPUTE2
    • Marchini J. Homepage of IMPUTE2. 2009.
    • (2009)
    • Marchini, J.1
  • 27
    • 84904634116 scopus 로고    scopus 로고
    • fcGENE: A Versatile Tool for Processing and Transforming SNP Datasets
    • Roshyara NR, Scholz M. fcGENE: A Versatile Tool for Processing and Transforming SNP Datasets. PLoS One. 2014;9:e97589.
    • (2014) PLoS One , vol.9 , pp. e97589
    • Roshyara, N.R.1    Scholz, M.2
  • 30
    • 0028152424 scopus 로고
    • A note on testing the Hardy-Weinberg law across strata
    • Troendle JF, Yu KF. A note on testing the Hardy-Weinberg law across strata. Ann Hum Genet. 1994;58(Pt 4):397-402.
    • (1994) Ann Hum Genet , vol.58 , pp. 397-402
    • Troendle, J.F.1    Yu, K.F.2
  • 31
    • 85019255032 scopus 로고    scopus 로고
    • Impact of Pre-imputation SNP-filtering on Genotype Imputation Results
    • Roshyara NR, Kirsten H, Horn K, Ahnert P, Scholz M. Impact of Pre-imputation SNP-filtering on Genotype Imputation Results. PLoS One. 2012;7(11):e50610.
    • (2012) PLoS One , vol.7 , Issue.11
    • Roshyara, N.R.1    Kirsten, H.2    Horn, K.3    Ahnert, P.4    Scholz, M.5
  • 33
    • 77953808087 scopus 로고    scopus 로고
    • Genotype imputation for genome-wide association studies
    • Marchini J, Howie B. Genotype imputation for genome-wide association studies. Nat Rev Genet. 2010;11:499-511.
    • (2010) Nat Rev Genet , vol.11 , pp. 499-511
    • Marchini, J.1    Howie, B.2
  • 34
    • 77956843366 scopus 로고    scopus 로고
    • Population Structure With Localized Haplotype Clusters
    • Browning SR, Weir BS. Population Structure With Localized Haplotype Clusters. Genetics. 2010;185:1337-44.
    • (2010) Genetics , vol.185 , pp. 1337-1344
    • Browning, S.R.1    Weir, B.S.2
  • 35
    • 0036911353 scopus 로고    scopus 로고
    • Interrogating a High-Density SNP Map for Signatures of Natural Selection
    • Akey JM. Interrogating a High-Density SNP Map for Signatures of Natural Selection. Genome Res. 2002;12:1805-14.
    • (2002) Genome Res , vol.12 , pp. 1805-1814
    • Akey, J.M.1
  • 36
    • 77749296886 scopus 로고    scopus 로고
    • ggplot2: Elegant Graphics for Data Analysis
    • (Use R!). New York NY: Springer
    • Wichmann H. ggplot2: Elegant Graphics for Data Analysis (Use R!). New York NY: Springer; 2009.
    • (2009)
    • Wichmann, H.1
  • 37
    • 0002282074 scopus 로고
    • A NEW MEASURE OF RANK CORRELATION
    • Kendall MG. A NEW MEASURE OF RANK CORRELATION. Biometrika. 1938;30:81-93.
    • (1938) Biometrika , vol.30 , pp. 81-93
    • Kendall, M.G.1
  • 38
    • 85018193345 scopus 로고    scopus 로고
    • Genotype imputation accuracy with different reference panels in admixed populations
    • Huang G-H, Tseng Y-C. Genotype imputation accuracy with different reference panels in admixed populations. BMC Proc. 2014;8 Suppl 1:S64.
    • (2014) BMC Proc , vol.8 , pp. S64
    • Huang, G.-H.1    Tseng, Y.-C.2
  • 39
    • 67651222400 scopus 로고    scopus 로고
    • A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
    • Howie BN, Donnelly P, Marchini J. A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies. PLoS Genet. 2009;5, e1000529.
    • (2009) PLoS Genet , vol.5
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 40
    • 84922011640 scopus 로고    scopus 로고
    • A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer
    • Al Olama AA, Kote-Jarai Z, Berndt SI, Conti DV, Schumacher F, Han Y, et al. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. Nat Genet. 2014;46:1103-9.
    • (2014) Nat Genet , vol.46 , pp. 1103-1109
    • Al Olama, A.A.1    Kote-Jarai, Z.2    Berndt, S.I.3    Conti, D.V.4    Schumacher, F.5    Han, Y.6
  • 41
    • 84946412694 scopus 로고    scopus 로고
    • Assessment of the Genetic Basis of Rosacea by Genome-Wide Association Study
    • Chang ALS, Raber I, Xu J, Li R, Spitale R, Chen J, et al. Assessment of the Genetic Basis of Rosacea by Genome-Wide Association Study. J Invest Dermatol. 2015;135(6):1548-55.
    • (2015) J Invest Dermatol , vol.135 , Issue.6 , pp. 1548-1555
    • Chang, A.L.S.1    Raber, I.2    Xu, J.3    Li, R.4    Spitale, R.5    Chen, J.6
  • 43
    • 84924363528 scopus 로고    scopus 로고
    • Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels
    • Van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, et al. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun. 2015;6:6065.
    • (2015) Nat Commun , vol.6 , pp. 6065
    • Van Leeuwen, E.M.1    Karssen, L.C.2    Deelen, J.3    Isaacs, A.4    Medina-Gomez, C.5    Mbarek, H.6
  • 44
    • 84901631426 scopus 로고    scopus 로고
    • Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics
    • Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, et al. Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics. PLoS Genet. 2014;10, e1004383.
    • (2014) PLoS Genet , vol.10
    • Giambartolomei, C.1    Vukcevic, D.2    Schadt, E.E.3    Franke, L.4    Hingorani, A.D.5    Wallace, C.6
  • 46
    • 84864417548 scopus 로고    scopus 로고
    • Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
    • Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 2012;44:955-9.
    • (2012) Nat Genet , vol.44 , pp. 955-959
    • Howie, B.1    Fuchsberger, C.2    Stephens, M.3    Marchini, J.4    Abecasis, G.R.5
  • 47
    • 84922051625 scopus 로고    scopus 로고
    • Performance of Genotype Imputation for Low Frequency and Rare Variants from the 1000 Genomes
    • Zheng H-F, Rong J-J, Liu M, Han F, Zhang X-W, Richards JB, et al. Performance of Genotype Imputation for Low Frequency and Rare Variants from the 1000 Genomes. PLoS One. 2015;10, e0116487.
    • (2015) PLoS One , vol.10
    • Zheng, H.-F.1    Rong, J.-J.2    Liu, M.3    Han, F.4    Zhang, X.-W.5    Richards, J.B.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.