Enhanced localization of genetic samples through linkage-disequilibrium correction

American Journal of Human Genetics

Volumn 92, Issue 6, 2013, Pages 882-894

  Baran, Yael ^a   Quintela, Inés ^b   Carracedo, Ángel ^b,c   Pasaniuc, Bogdan ^d   Halperin, Eran ^a,e  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^c Instituto de Salud Carlos III   (Spain)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENETIC MARKER; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; GENETIC MARKERS; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE; SPAIN;

EID: 84878885949     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2013.04.023     Document Type: Article

References (33)

1. A.L. Price, N.A. Zaitlen, D. Reich, and N. Patterson New approaches to population stratification in genome-wide association studies Nat. Rev. Genet. 11 2010 459 463
2. M.F. Seldin, B. Pasaniuc, and A.L. Price New approaches to disease mapping in admixed populations Nat. Rev. Genet. 12 2011 523 528
3. A.L. Price, N.J. Patterson, R.M. Plenge, M.E. Weinblatt, N.A. Shadick, and D. Reich Principal components analysis corrects for stratification in genome-wide association studies Nat. Genet. 38 2006 904 909
4. J.P. Jarvis, L.B. Scheinfeldt, S. Soi, C. Lambert, L. Omberg, B. Ferwerda, A. Froment, J.M. Bodo, W. Beggs, and G. Hoffman Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies PLoS Genet. 8 2012 e1002641
5. K. Bryc, C. Velez, T. Karafet, A. Moreno-Estrada, A. Reynolds, A. Auton, M. Hammer, C.D. Bustamante, and H. Ostrer Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations Proc. Natl. Acad. Sci. USA 107 Suppl 2 2010 8954 8961
6. A.G. Hinch, A. Tandon, N. Patterson, Y. Song, N. Rohland, C.D. Palmer, G.K. Chen, K. Wang, S.G. Buxbaum, and E.L. Akylbekova The landscape of recombination in African Americans Nature 476 2011 170 175
7. D. Wegmann, D.E. Kessner, K.R. Veeramah, R.A. Mathias, D.L. Nicolae, L.R. Yanek, Y.V. Sun, D.G. Torgerson, N. Rafaels, and T. Mosley Recombination rates in admixed individuals identified by ancestry-based inference Nat. Genet. 43 2011 847 853
8. S. Gravel, B.M. Henn, R.N. Gutenkunst, A.R. Indap, G.T. Marth, A.G. Clark, F. Yu, R.A. Gibbs, C.D. Bustamante 1000 Genomes Project Demographic history and rare allele sharing among human populations Proc. Natl. Acad. Sci. USA 108 2011 11983 11988
9. J.J. Yang, C. Cheng, M. Devidas, X. Cao, Y. Fan, D. Campana, W. Yang, G. Neale, N.J. Cox, and P. Scheet Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia Nat. Genet. 43 2011 237 241
10. P. Menozzi, A. Piazza, and L. Cavalli-Sforza Synthetic maps of human gene frequencies in Europeans Science 201 1978 786 792
11. W.Y. Yang, J. Novembre, E. Eskin, and E. Halperin A model-based approach for analysis of spatial structure in genetic data Nat. Genet. 44 2012 725 731
12. A.L. Price, M.E. Weale, N. Patterson, S.R. Myers, A.C. Need, K.V. Shianna, D. Ge, J.I. Rotter, E. Torres, and K.D. Taylor Long-range LD can confound genome scans in admixed populations Am. J. Hum. Genet. 83 2008 132 135 author reply 135-139
13. C. Tian, R.M. Plenge, M. Ransom, A. Lee, P. Villoslada, C. Selmi, L. Klareskog, A.E. Pulver, L. Qi, P.K. Gregersen, and M.F. Seldin Analysis and application of European genetic substructure using 300 K SNP information PLoS Genet. 4 2008 e4
14. M.R. Nelson, K. Bryc, K.S. King, A. Indap, A.R. Boyko, J. Novembre, L.P. Briley, Y. Maruyama, D.M. Waterworth, and G. Waeber The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research Am. J. Hum. Genet. 83 2008 347 358
15. N.A. Johnson, M.A. Coram, M.D. Shriver, I. Romieu, G.S. Barsh, S.J. London, and H. Tang Ancestral components of admixed genomes in a Mexican cohort PLoS Genet. 7 2011 e1002410
16. Y. Baran, B. Pasaniuc, S. Sankararaman, D.G. Torgerson, C. Gignoux, C. Eng, W. Rodriguez-Cintron, R. Chapela, J.G. Ford, and P.C. Avila Fast and accurate inference of local ancestry in Latino populations Bioinformatics 28 2012 1359 1367
17. A.L. Price, A. Tandon, N. Patterson, K.C. Barnes, N. Rafaels, I. Ruczinski, T.H. Beaty, R. Mathias, D. Reich, and S. Myers Sensitive detection of chromosomal segments of distinct ancestry in admixed populations PLoS Genet. 5 2009 e1000519
18. X. Wen, and M. Stephens Using linear predictors to impute allele frequencies from summary or pooled genotype data Ann Appl Stat 4 2010 1158 1182
19. A. Menelaou, and J. Marchini Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold Bioinformatics 29 2013 84 91
20. C. Churchhouse, and J. Marchini Multiway admixture deconvolution using phased or unphased ancestral panels Genet. Epidemiol. 37 2013 1 12
21. J. Novembre, T. Johnson, K. Bryc, Z. Kutalik, A.R. Boyko, A. Auton, A. Indap, K.S. King, S. Bergmann, and M.R. Nelson Genes mirror geography within Europe Nature 456 2008 98 101
22. C. Wang, S. Zöllner, and N.A. Rosenberg A quantitative comparison of the similarity between genes and geography in worldwide human populations PLoS Genet. 8 2012 e1002886
23. N. Patterson, A.L. Price, and D. Reich Population structure and eigenanalysis PLoS Genet. 2 2006 e190
24. S.R. Browning, and B.L. Browning Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering Am. J. Hum. Genet. 81 2007 1084 1097
25. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A. Ferreira, D. Bender, J. Maller, P. Sklar, P.I. de Bakker, M.J. Daly, and P.C. Sham PLINK: a tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet. 81 2007 559 575
26. M.D. Shumaker, and P. Bryan Computing under the open sky Sky Telescope 68 1984 158
27. R.W. Sinnott Virtues of the haversine Sky Telescope 68 1984 159
28. J.K. Pritchard, and M. Przeworski Linkage disequilibrium in humans: models and data Am. J. Hum. Genet. 69 2001 1 14
29. J.H. Sul, and E. Eskin Mixed models can correct for population structure for genomic regions under selection Nat. Rev. Genet. 14 2013 300
30. A. Brisbin, K. Bryc, J. Byrnes, F. Zakharia, L. Omberg, J. Degenhardt, A. Reynolds, H. Ostrer, J.G. Mezey, and C.D. Bustamante PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations Hum. Biol. 84 2012 343 364
31. A.B. Lee, D. Luca, L. Klei, B. Devlin, and K. Roeder Discovering genetic ancestry using spectral graph theory Genet. Epidemiol. 34 2010 51 59
32. B.E. Engelhardt, and M. Stephens Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis PLoS Genet. 6 2010 e1001117
33. D.H. Alexander, J. Novembre, and K. Lange Fast model-based estimation of ancestry in unrelated individuals Genome Res. 19 2009 1655 1664