Inference of Population Structure using Dense Haplotype Data

PLoS Genetics - Tập 8 Số 1 - Trang e1002453
Daniel J. Lawson1, Garrett Hellenthal2, Simon Myers3, Daniel Falush4,5
1Department of Mathematics, University of Bristol, Bristol, United Kingdom
2Wellcome Trust Center for Human Genetics, Oxford, United Kingdom
3Department of Statistics, University of Oxford, Oxford, United Kingdom
4Environmental Research Institute, University College Cork, Cork, Ireland
5Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

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P Menozzi, 1978, Synthetic maps of human gene frequencies in europeans., Science, 201, 786, 10.1126/science.356262

JK Pritchard, 2000, Inference of population structure using multilocus genotype data., Genetics, 155, 945, 10.1093/genetics/155.2.945

J Novembre, 2008, Interpreting principal component analyses of spatial population genetic variation., Nature Genetics, 40, 646, 10.1038/ng.139

G McVean, 2009, A Genealogical Interpretation of Principal Components Analysis., PLoS Genet, 5, e1000686, 10.1371/journal.pgen.1000686

AL Price, 2006, Principal components analysis corrects for stratification in genome-wide association studies., Nature Genetics, 38, 904, 10.1038/ng1847

D Reich, 2009, Reconstructing Indian population history., Nature, 461, 489, 10.1038/nature08365

J Novembre, 2008, Genes mirror geography within Europe., Nature, 456, 98, 10.1038/nature07331

NA Rosenberg, 2001, Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds., Genetics, 159, 699, 10.1093/genetics/159.2.699

JZ Li, 2008, Worldwide human relationships inferred from genome-wide patterns of variation., Science, 319, 1100, 10.1126/science.1153717

SA Tishkoff, 2009, The genetic structure and history of africans and african americans., Science, 324, 1035, 10.1126/science.1172257

J Corander, 2003, Bayesian analysis of genetic differentiation between populations., Genetics, 163, 367, 10.1093/genetics/163.1.367

D Falush, 2003, Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies., Genetics, 164, 1567, 10.1093/genetics/164.4.1567

G Guillot, 2005, A spatial statistical model for landscape genetics., Genetics, 170, 1261, 10.1534/genetics.104.033803

H Tang, 2005, Estimation of individual admixture: Analytical and study design considerations., Genetic Epidemiology, 28, 289, 10.1002/gepi.20064

DH Alexander, 2009, Fast model-based estimation of ancestry in unrelated individuals., Genome Research, 19, 1655, 10.1101/gr.094052.109

E Durand, 2009, Spatial inference of admixture proportions and secondary contact zones., Molecular Biology and Evolution, 26, 1963, 10.1093/molbev/msp106

T Jombart, 2010, Discriminant analysis of principal components: a new method for the analysis of genetically structured populations., BMC Genetics, 11, 94, 10.1186/1471-2156-11-94

KJ Dawson, 2001, A bayesian approach to the identification of panmictic populations and the assignment of individuals., Genetical Research, 78, 59, 10.1017/S001667230100502X

J Pella, 2006, The gibbs and split–merge sampler for population mixture analysis from genetic data with incomplete baselines., Can J Fish Aquat Sci, 63, 576, 10.1139/f05-224

T Niu, 2004, Algorithms for inferring haplotypes., Genetic Epidemiology, 27, 334, 10.1002/gepi.20024

P Scheet, 2006, A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase., American Journal of Human Genetics, 78, 629, 10.1086/502802

SR Browning, 2007, Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering., American Journal of Human Genetics, 81, 1084, 10.1086/521987

HC Fan, 2011, Whole-genome molecular haplotyping of single cells., Nature, 29, 51

JO Kitzman, 2011, Haplotype-resolved genome sequencing of a gujarati indian individual., Nature, 29, 59

DF Conrad, 2006, A worldwide survey of haplotype variation and linkage disequilibrium in the human genome., Nature Genetics, 38, 1251, 10.1038/ng1911

2007, A second generation human haplotype map of over 3.1 million snps., Nature, 449, 851, 10.1038/nature06258

G Hellenthal, 2008, Inferring Human Colonization History Using a Copying Model., PLoS Genet, 4, e1000078, 10.1371/journal.pgen.1000078

M Jakobsson, 2008, Genotype, haplotype and copy-number variation in worldwide human populations., Nature, 451, 998, 10.1038/nature06742

SR Browning, 2010, Population structure with localized haplotype clusters., Genetics, 185, 1337, 10.1534/genetics.110.116681

P Donnelly, 2010, The coalescent and its descendants., arXiv, 1006.1514v1

LM Gattepaille, 2011, Combining markers into haplotypes can improve population structure inference., Genetics

H Tang, 2006, Reconstructing genetic ancestry blocks in admixed individuals., American Journal of Human Genetics, 79, 1, 10.1086/504302

S Sankararaman, 2008, Estimating local ancestry in admixed populations., American Journal of Human Genetics, 82, 290, 10.1016/j.ajhg.2007.09.022

AL Price, 2009, Sensitive detection of chromosomal segments of distinct ancestry in admixed populations., PLoS Genet, 5, e1000519, 10.1371/journal.pgen.1000519

N Li, 2003, Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data., Genetics, 165, 2213, 10.1093/genetics/165.4.2213

AP Dempster, 1977, Maximum likelihood from incomplete data via the em algorithm., J Roy Stat Soc B, 39, 1, 10.1111/j.2517-6161.1977.tb01600.x

JP Huelsenbeck, 2007, Inference of population structure under a dirichlet process model., Genetics, 175, 1787, 10.1534/genetics.106.061317

D Gamerman, 1997, Markov Chain Monte Carlo: Stochastic simulation for Bayesian inference

N Cardin, 2007, Approximating the Coalescent with Recombination.

G McVean, 2005, Approximating the coalescent with recombination., Philos Trans R Soc Lond B Biol Sci, 360, 1387, 10.1098/rstb.2005.1673

N Patterson, 2006, Population structure and eigenanalysis., PLoS Genet, 2, e190, 10.1371/journal.pgen.0020190

R Hernandez, 2008, A flexible forward simulator for populations subject to selection and demography., Bioinformatics, 24, 2786, 10.1093/bioinformatics/btn522

BE Engelhardt, 2010, Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis., PLoS Genet, 6, e1001117, 10.1371/journal.pgen.1001117

JK Pickrell, 2009, Signals of recent positive selection in a worldwide sample of human populations., Genome Research, 19, 826, 10.1101/gr.087577.108

N Rosenberg, 2002, The genetic structure of human populations., Science, 298, 2381, 10.1126/science.1078311

L Zhivotovsky, 2003, Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers., American Journal of Human Genetics, 72, 1171, 10.1086/375120

EE Bacon, 1951, The inquiry into the history of the hazara mongols of afghanistan., Southwestern Journal of Anthropology, 7, 230, 10.1086/soutjanth.7.3.3628602

M Pellecchia, 2007, The mystery of Etruscan origins: novel clues from bos taurus mitochondrial dna., Proceedings of the Royal Society B: Biological Sciences, 274, 1175, 10.1098/rspb.2006.0258

B Wen, 2004, Genetic evidence supports demic diffusion of han culture., Nature, 431, 302, 10.1038/nature02878

N Patterson, 2006, Population Structure and Eigenanalysis., PLoS Genet, 2, e190, 10.1371/journal.pgen.0020190

2010, A map of human genome variation from populationscale sequencing., Nature, 467, 1061, 10.1038/nature09534

RR Hudson, 2002, Generating samples under a wright-fisher neutral model., Bioinformatics, 18, 337, 10.1093/bioinformatics/18.2.337