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Volumn 10, Issue , 2009, Pages

Iterative pruning PCA improves resolution of highly structured populations

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONALLY EFFICIENT; EVOLUTIONARY FACTORS; GENETIC VARIATION; NON-RANDOM PATTERNS; POPULATION STRUCTURES; PRINCIPAL COMPONENTS ANALYSIS; SIMPLE STRUCTURES; STRUCTURED POPULATION;

EID: 71949111362     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-382     Document Type: Article
Times cited : (32)

References (43)
  • 1
    • 0037442092 scopus 로고    scopus 로고
    • Population stratification and spurious allelic association
    • 10.1016/S0140-6736(03)12520-2, 12598158
    • Cardon LR, Palmer LJ. Population stratification and spurious allelic association. Lancet 2003, 361(9357):598-604. 10.1016/S0140-6736(03)12520-2, 12598158.
    • (2003) Lancet , vol.361 , Issue.9357 , pp. 598-604
    • Cardon, L.R.1    Palmer, L.J.2
  • 2
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • 1461096, 10835412
    • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945-959. 1461096, 10835412.
    • (2000) Genetics , vol.155 , Issue.2 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 3
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • 10.1038/nature04226, 1880871, 16255080
    • Consortium IH A haplotype map of the human genome. Nature 2005, 437(7063):1299-1320. 10.1038/nature04226, 1880871, 16255080.
    • (2005) Nature , vol.437 , Issue.7063 , pp. 1299-1320
  • 4
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    • 1462648, 12930761
    • Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164(4):1567-1587. 1462648, 12930761.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 5
    • 18444396148 scopus 로고    scopus 로고
    • Properties of structured association approaches to detecting population stratification
    • 10.1159/000083030, 15711089
    • Purcell S, Sham P. Properties of structured association approaches to detecting population stratification. Human heredity 2004, 58(2):93-107. 10.1159/000083030, 15711089.
    • (2004) Human heredity , vol.58 , Issue.2 , pp. 93-107
    • Purcell, S.1    Sham, P.2
  • 6
    • 33747426655 scopus 로고    scopus 로고
    • PSMIX: an R package for population structure inference via maximum likelihood method
    • 10.1186/1471-2105-7-317, 1550430, 16792813
    • Wu B, Liu N, Zhao H. PSMIX: an R package for population structure inference via maximum likelihood method. BMC bioinformatics 2006, 7:317. 10.1186/1471-2105-7-317, 1550430, 16792813.
    • (2006) BMC bioinformatics , vol.7 , pp. 317
    • Wu, B.1    Liu, N.2    Zhao, H.3
  • 7
    • 17644402806 scopus 로고    scopus 로고
    • Estimation of individual admixture: analytical and study design considerations
    • 10.1002/gepi.20064, 15712363
    • Tang H, Peng J, Wang P, Risch NJ. Estimation of individual admixture: analytical and study design considerations. Genetic epidemiology 2005, 28(4):289-301. 10.1002/gepi.20064, 15712363.
    • (2005) Genetic epidemiology , vol.28 , Issue.4 , pp. 289-301
    • Tang, H.1    Peng, J.2    Wang, P.3    Risch, N.J.4
  • 8
    • 33747078134 scopus 로고    scopus 로고
    • Bayesian identification of admixture events using multilocus molecular markers
    • Corander J, Marttinen P. Bayesian identification of admixture events using multilocus molecular markers. Molecular ecology 2006, 15(10):2833-2843.
    • (2006) Molecular ecology , vol.15 , Issue.10 , pp. 2833-2843
    • Corander, J.1    Marttinen, P.2
  • 9
    • 62349132559 scopus 로고    scopus 로고
    • Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
    • 10.1186/1471-2105-9-539, 2629778, 19087322
    • Corander J, Marttinen P, Siren J, Tang J. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC bioinformatics 2008, 9:539. 10.1186/1471-2105-9-539, 2629778, 19087322.
    • (2008) BMC bioinformatics , vol.9 , pp. 539
    • Corander, J.1    Marttinen, P.2    Siren, J.3    Tang, J.4
  • 10
    • 34547883224 scopus 로고    scopus 로고
    • Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study
    • Chen C, Durand E, Forbes F, François O. Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study. Molecular Ecology Notes 2007, 7(5):747-756.
    • (2007) Molecular Ecology Notes , vol.7 , Issue.5 , pp. 747-756
    • Chen, C.1    Durand, E.2    Forbes, F.3    François, O.4
  • 12
    • 59349095257 scopus 로고    scopus 로고
    • Accurate Inference of Subtle Population STructure (and Other Genetic Discontinuities) Using Proncipal Coordinates
    • 10.1371/journal.pone.0004269, 2625398, 19172174
    • Reeves PA, Richards CM. Accurate Inference of Subtle Population STructure (and Other Genetic Discontinuities) Using Proncipal Coordinates. PLoS ONE 2009, 4(1). 10.1371/journal.pone.0004269, 2625398, 19172174.
    • (2009) PLoS ONE , vol.4 , Issue.1
    • Reeves, P.A.1    Richards, C.M.2
  • 13
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • 10.1371/journal.pgen.0020190, 1713260,1713260, 17194218
    • Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS genetics 2006, 2(12):e190. 10.1371/journal.pgen.0020190, 1713260,1713260, 17194218.
    • (2006) PLoS genetics , vol.2 , Issue.12
    • Patterson, N.1    Price, A.L.2    Reich, D.3
  • 14
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • 10.1038/ng1847, 16862161
    • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics 2006, 38(8):904-909. 10.1038/ng1847, 16862161.
    • (2006) Nature genetics , vol.38 , Issue.8 , pp. 904-909
    • Price, A.L.1    Patterson, N.J.2    Plenge, R.M.3    Weinblatt, M.E.4    Shadick, N.A.5    Reich, D.6
  • 15
    • 44849091227 scopus 로고    scopus 로고
    • A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation
    • 10.1371/journal.pgen.1000074, 2367449, 18483556
    • Han J, Kraft P, Nan H, Guo Q, Chen C, Qureshi A, Hankinson SE, Hu FB, Duffy DL, Zhao ZZ. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. PLoS genetics 2008, 4(5):e1000074. 10.1371/journal.pgen.1000074, 2367449, 18483556.
    • (2008) PLoS genetics , vol.4 , Issue.5
    • Han, J.1    Kraft, P.2    Nan, H.3    Guo, Q.4    Chen, C.5    Qureshi, A.6    Hankinson, S.E.7    Hu, F.B.8    Duffy, D.L.9    Zhao, Z.Z.10
  • 16
    • 43249083380 scopus 로고    scopus 로고
    • A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci
    • 10.1371/journal.pgen.1000041, 2274885, 18369459
    • Liu Y, Helms C, Liao W, Zaba LC, Duan S, Gardner J, Wise C, Miner A, Malloy MJ, Pullinger CR. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. PLoS genetics 2008, 4(3):e1000041. 10.1371/journal.pgen.1000041, 2274885, 18369459.
    • (2008) PLoS genetics , vol.4 , Issue.3
    • Liu, Y.1    Helms, C.2    Liao, W.3    Zaba, L.C.4    Duan, S.5    Gardner, J.6    Wise, C.7    Miner, A.8    Malloy, M.J.9    Pullinger, C.R.10
  • 18
    • 17044376078 scopus 로고    scopus 로고
    • Subspace Clustering for high dimensional data: A review
    • Parsons L, Haque E, Liu H. Subspace Clustering for high dimensional data: A review. Sigkdd Explorations 2004, 6(1):15.
    • (2004) Sigkdd Explorations , vol.6 , Issue.1 , pp. 15
    • Parsons, L.1    Haque, E.2    Liu, H.3
  • 19
    • 39749104719 scopus 로고    scopus 로고
    • AWclust: point-and-click software for non-parametric population structure analysis
    • 10.1186/1471-2105-9-77, 2253519, 18237431
    • Gao X, Starmer JD. AWclust: point-and-click software for non-parametric population structure analysis. BMC bioinformatics 2008, 9:77. 10.1186/1471-2105-9-77, 2253519, 18237431.
    • (2008) BMC bioinformatics , vol.9 , pp. 77
    • Gao, X.1    Starmer, J.D.2
  • 20
    • 60849085181 scopus 로고    scopus 로고
    • PCA-based population structure inference with generic clustering algorithms
    • 10.1186/1471-2105-10-S1-S73, 2648762, 19208178
    • Lee C, Abdool A, Huang CH. PCA-based population structure inference with generic clustering algorithms. BMC bioinformatics 2009, 10(Suppl 1):S73. 10.1186/1471-2105-10-S1-S73, 2648762, 19208178.
    • (2009) BMC bioinformatics , vol.10 , Issue.SUPPL. 1
    • Lee, C.1    Abdool, A.2    Huang, C.H.3
  • 21
    • 33746329940 scopus 로고    scopus 로고
    • A non-parametric approach to population structure inference using multilocus genotypes
    • Liu N, Zhao H. A non-parametric approach to population structure inference using multilocus genotypes. Human genomics 2006, 2(6):353-364.
    • (2006) Human genomics , vol.2 , Issue.6 , pp. 353-364
    • Liu, N.1    Zhao, H.2
  • 23
    • 0004236492 scopus 로고    scopus 로고
    • Matrix computations
    • Baltimore: The Johns Hopkins University Press, 3
    • Golub GH, Van Loan FC. matrix computations. 1996, Baltimore: The Johns Hopkins University Press, 3.
    • (1996)
    • Golub, G.H.1    Van Loan, F.C.2
  • 25
    • 40749138264 scopus 로고    scopus 로고
    • On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants
    • 10.1016/j.ajhg.2007.11.003, 2427172, 18252225
    • Luca D, Ringquist S, Klei L, Lee AB, Gieger C, Wichmann HE, Schreiber S, Krawczak M, Lu Y, Styche A. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. American journal of human genetics 2008, 82(2):453-463. 10.1016/j.ajhg.2007.11.003, 2427172, 18252225.
    • (2008) American journal of human genetics , vol.82 , Issue.2 , pp. 453-463
    • Luca, D.1    Ringquist, S.2    Klei, L.3    Lee, A.B.4    Gieger, C.5    Wichmann, H.E.6    Schreiber, S.7    Krawczak, M.8    Lu, Y.9    Styche, A.10
  • 26
    • 0035532141 scopus 로고    scopus 로고
    • Estimating the number of clusters in a dataset via the gap statistic
    • Tibshirani RWG, Hastie T. Estimating the number of clusters in a dataset via the gap statistic. Journal Royal Statistical Soc B 2001, 63:411-423.
    • (2001) Journal Royal Statistical Soc B , vol.63 , pp. 411-423
    • Tibshirani, R.W.G.1    Hastie, T.2
  • 27
    • 0004008854 scopus 로고
    • Pattern Recognition with Fuzzy Objective Function Algorithms
    • New York: Plenum Press
    • Bezdec JC. Pattern Recognition with Fuzzy Objective Function Algorithms. 1981, New York: Plenum Press.
    • (1981)
    • Bezdec, J.C.1
  • 28
    • 84888300255 scopus 로고    scopus 로고
    • Download Structure 2.2
    • Download Structure 2.2. , http://pritch.bsd.uchicago.edu/software/structure2_2.html
  • 29
    • 84888307792 scopus 로고    scopus 로고
    • Installing BAPS to XP/Windows 2000 systems
    • Installing BAPS to XP/Windows 2000 systems. , http://web.abo.fi/fak/mnf/mate/jc/software/baps_xp.html
  • 30
    • 84888297555 scopus 로고    scopus 로고
    • AWclust
    • AWclust. , http://awclust.sourceforge.net/
  • 31
    • 34547830810 scopus 로고    scopus 로고
    • GENOME: a rapid coalescent-based whole genome simulator
    • 10.1093/bioinformatics/btm138, 17459963
    • Liang L, Zollner S, Abecasis GR. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics (Oxford, England) 2007, 23(12):1565-1567. 10.1093/bioinformatics/btm138, 17459963.
    • (2007) Bioinformatics (Oxford, England) , vol.23 , Issue.12 , pp. 1565-1567
    • Liang, L.1    Zollner, S.2    Abecasis, G.R.3
  • 32
    • 0003751736 scopus 로고
    • Mathematical Population Genetics
    • Berlin: Springer
    • Ewens WJ. Mathematical Population Genetics. 1979, Berlin: Springer.
    • (1979)
    • Ewens, W.J.1
  • 33
    • 84870445213 scopus 로고    scopus 로고
    • International HapMap Project
    • International HapMap Project. , http://hapmap.org
  • 34
    • 84888306956 scopus 로고    scopus 로고
    • FTP site for downloading bovine SNPs
    • FTP site for downloading bovine SNPs. , ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/snp/Btau20040927
  • 35
    • 84888286298 scopus 로고    scopus 로고
    • Bovine Genome Project
    • Bovine Genome Project. , http://www.hgsc.bcm.tmc.edu/projects/bovine/index.html
  • 37
    • 84888293851 scopus 로고    scopus 로고
    • Breeds of Livestock, Cattle: (Bos)
    • Breeds of Livestock, Cattle: (Bos). , http://www.ansi.okstate.edu/breeds/cattle/
  • 38
    • 42649088044 scopus 로고    scopus 로고
    • Principal component analysis of genetic data
    • 10.1038/ng0508-491, 18443580
    • Reich D, Price AL, Patterson N. Principal component analysis of genetic data. Nature genetics 2008, 40(5):491-492. 10.1038/ng0508-491, 18443580.
    • (2008) Nature genetics , vol.40 , Issue.5 , pp. 491-492
    • Reich, D.1    Price, A.L.2    Patterson, N.3
  • 39
    • 34848879778 scopus 로고    scopus 로고
    • PCA-correlated SNPs for structure identification in worldwide human populations
    • 10.1371/journal.pgen.0030160, 1988848,1988848, 17892327
    • Paschou P, Ziv E, Burchard EG, Choudhry S, Rodriguez-Cintron W, Mahoney MW, Drineas P. PCA-correlated SNPs for structure identification in worldwide human populations. PLoS genetics 2007, 3(9):1672-1686. 10.1371/journal.pgen.0030160, 1988848,1988848, 17892327.
    • (2007) PLoS genetics , vol.3 , Issue.9 , pp. 1672-1686
    • Paschou, P.1    Ziv, E.2    Burchard, E.G.3    Choudhry, S.4    Rodriguez-Cintron, W.5    Mahoney, M.W.6    Drineas, P.7
  • 40
    • 33645859299 scopus 로고    scopus 로고
    • What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity
    • 10.1111/j.1365-294X.2006.02890.x, 16629801
    • Waples RS, Gaggiotti O. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular ecology 2006, 15(6):1419-1439. 10.1111/j.1365-294X.2006.02890.x, 16629801.
    • (2006) Molecular ecology , vol.15 , Issue.6 , pp. 1419-1439
    • Waples, R.S.1    Gaggiotti, O.2
  • 42
    • 41949141213 scopus 로고    scopus 로고
    • Data Clustering: Theory, Algorithms, and Applications
    • SIAM (Society for Industrial and Applied Mathematics), Philadephia
    • Guojun Gan CM, Jianhong W. Data Clustering: Theory, Algorithms, and Applications. 2007, SIAM (Society for Industrial and Applied Mathematics), Philadephia.
    • (2007)
    • Guojun Gan, C.M.1    Jianhong, W.2


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