Dating the age of admixture via wavelet transform analysis of genome-wide data

Genome Biology

Volumn 12, Issue 2, 2011, Pages

  Pugach, Irina ^a   Matveyev, Rostislav ^b   Wollstein, Andreas ^c,d   Kayser, Manfred ^d   Stoneking, Mark ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c UNIVERSITY OF COLOGNE   (Germany)

^d ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; GENE LINKAGE DISEQUILIBRIUM; GENE STRUCTURE; GENETIC VARIABILITY; GENOME ANALYSIS; POPULATION GENETIC STRUCTURE; PRINCIPAL COMPONENT ANALYSIS; RACE DIFFERENCE; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; WAVEFORM; ALGORITHM; CAUCASIAN; FEMALE; FIJI; GENETIC ASSOCIATION; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; MALE; METHODOLOGY; NEGRO; PHYLOGEOGRAPHY; POLYNESIA; POPULATION DYNAMICS; POPULATION GENETICS; STATISTICS; WAVELET ANALYSIS;

AFRICAN CONTINENTAL ANCESTRY GROUP; ALGORITHMS; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; FIJI; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYNESIA; POPULATION DYNAMICS; WAVELET ANALYSIS;

EID: 79951950847     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-2-r19     Document Type: Article

References (43)

1. Myles S, Davison D, Barrett J, Stoneking M, Timpson N. Worldwide population differentiation at disease-associated SNPs. BMC Medical Genomics 2008, 1:22. 10.1186/1755-8794-1-22, 2440747, 18533027.
2. Choudhry S, Taub M, Mei R, Rodriguez-Santana J, Rodriguez-Cintron W, Shriver M, Ziv E, Risch N, Burchard E. Genome-wide screen for asthma in Puerto Ricans: evidence for association with 5q23 region. Human Genetics 2008, 123:455-468. 10.1007/s00439-008-0495-7, 2664533, 18401594.
3. Chakraborty R, Weiss KM. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proceedings of the National Academy of Sciences of the United States of America 1988, 85:9119-9123. 10.1073/pnas.85.23.9119, 282675, 3194414.
4. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, OBrien SJ, Altshuler D, Daly MJ, Reich D. Methods for high-density admixture mapping of disease genes. American Journal of Human Genetics 2004, 74:979-1000. 10.1086/420871, 1181990, 15088269.
5. Cheng CY, Kao WHL, Patterson N, Tandon A, Haiman CA, Harris TB, Xing C, John EM, Ambrosone CB, Brancati FL, Coresh J, Press MF, Parekh RS, Klag MJ, Meoni LA, Hsueh WC, Fejerman L, Pawlikowska L, Freedman ML, Jandorf LH, Bandera EV, Ciupak GL, Nalls MA, Akylbekova EL, Orwoll ES, Leak TS, Miljkovic I, Li R, Ursin G, Bernstein L, et al. Admixture mapping of 15,280 African Americans identifies obesity susceptibility loci on chromosomes 5 and X. PLoS Genetics 2009, 5:e1000490. 10.1371/journal.pgen.1000490, 2679192, 19461885.
6. Kayser M, Brauer S, Cordaux R, Casto A, Lao O, Zhivotovsky LA, Moyse-Faurie C, Rutledge RB, Schiefenhoevel W, Gil D, Lin AA, Underhill PA, Oefner PJ, Trent RJ, Stoneking M. Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the pacific. Molecular Biology and Evolution 2006, 23:2234-2244. 10.1093/molbev/msl093, 16923821.
7. Hellenthal G, Auton A, Falush D. Inferring human colonization history using a copying model. PLoS Genetics 2008, 4:e1000078. 10.1371/journal.pgen.1000078, 2367454, 18497854.
8. Reich D, Thangaraj K, Patterson N, Price AL, Singh L. Reconstructing Indian population history. Nature 2009, 461:489-494. 10.1038/nature08365, 2842210, 19779445.
9. Tang H, Choudhry S, Mei R, Morgan M, Rodriguez-Cintron W, Burchard EG, Risch NJ. Recent genetic selection in the ancestral admixture of Puerto Ricans. American Journal of Human Genetics 2007, 81:626-633. 10.1086/520769, 1950843, 17701908.
10. Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe C, Tishkoff SA, Bustamante CD. Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci U S A 2010, 107:786-791. 10.1073/pnas.0909559107, 2818934, 20080753.
11. Bertorelle G, Excoffier L. Inferring admixture proportions from molecular data. Molecular Biology and Evolution 1998, 15:1298-1311.
12. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164:1567-1587. 1462648, 12930761.
13. Tang H, Peng J, Wang P, Risch NJ. Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 2005, 28:289-301. 10.1002/gepi.20064, 15712363.
14. Tang H, Coram M, Wang P, Zhu X, Risch N. Reconstructing genetic ancestry blocks in admixed individuals. American Journal of Human Genetics 2006, 79:1-12. 10.1086/504302, 1474129, 16773560.
15. Sankararaman S, Sridhar S, Kimmel G, Halperin E. Estimating local ancestry in admixed populations. American Journal of Human Genetics 2008, 82:290-303. 10.1016/j.ajhg.2007.09.022, 2664993, 18252211.
16. Sankararaman S, Kimmel G, Halperin E, Jordan MI. On the inference of ancestries in admixed populations. Genome Research 2008, 18:668-675. 10.1101/gr.072751.107, 2279254, 18353809.
17. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genetics 2009, 5:e1000519. 10.1371/journal.pgen.1000519, 2689842, 19543370.
18. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008, 319:1100-1104. 10.1126/science.1153717, 18292342.
19. Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking M, Kayser M. Demographic history of Oceania inferred from genome-wide data. Current Biology 2010, 20:1983-1992. 10.1016/j.cub.2010.10.040, 21074440.
20. McVean G. A genealogical interpretation of principal components analysis. PLoS Genetics 2009, 5:e1000686. 10.1371/journal.pgen.1000686, 2757795, 19834557.
21. Andrés AM, Clark A, Shimmin L, Boerwinkle E, Sing CF, Hixson JE. Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genetic Epidemiology 2007, 31:659-671. 2291540, 17922479.
22. Mallat S. A Wavelet Tour of Signal Processing 2008, Academic Press, 3.
23. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. A fine-scale map of recombination rates and hotspots across the human genome. Science 2005, 310:321-324. 10.1126/science.1117196, 16224025.
24. Consortium IH. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449:851-861. 10.1038/nature06258, 2689609, 17943122.
25. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K. A high-resolution recombination map of the human genome. Nature Genetics 2002, 31:241-247.
26. Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Wood fine K, Spencer CCA, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell R. The DNA sequence and biological annotation of human chromosome 1. Nature 2006, 441:315-321. 10.1038/nature04727, 16710414.
27. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Research 2005, 15:1576-1583. 10.1101/gr.3709305, 1310645, 16251467.
28. Sabatti C, Risch N. Homozygosity and linkage disequilibrium. Genetics 2002, 160:1707-1719. 1462072, 11973323.
29. International HapMap Project. , http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2009-01phaseIII/
30. International HapMap Project. , http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/?N=D
31. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
32. HGDP CEPH Genotype Database. , ftp://ftp.cephb.fr/hgdp_supp1/
33. Fenner JN. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. American Journal of Physical Anthropology 2005, 128:415-423. 10.1002/ajpa.20188, 15795887.
34. R: A Language and Environment for Statistical Computing. , http://www.R-project.org
35. StepPCO Software. , http://bioinf.eva.mpg.de/download/StepPCO/
36. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, de Thé G, Essex M, Sankalé JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishko SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Ha fer DA, Altshuler D, Gilbert DA, et al. A high-density admixture map for disease gene discovery in African Americans. American Journal of Human Genetics 2004, 74:1001-1013. 10.1086/420856, 1181963, 15088270.
37. Lind J, Hutcheson-Dilks H, Williams S, Moore J, Essex M, Ruiz-Pesini E, Wallace D, Tishko S, Obrien S, Smith M. Elevated male European and female African contributions to the genomes of African American individuals. Human Genetics 2007, 120:713-722. 10.1007/s00439-006-0261-7, 17006671.
38. Friedlaender JS, Friedlaender FR, Reed FA, Kidd KK, Kidd JR, Chambers GK, Lea RA, Loo JH, Koki G, Hodgson JA, Merriwether DA, Weber JL. The genetic structure of pacific islanders. PLoS Genetics 2008, 4:e19. 10.1371/journal.pgen.0040019, 2211537, 18208337.
39. Kayser M, Lao O, Saar K, Brauer S, Wang X, Nürnberg P, Trent RJ, Stoneking M. Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. American Journal of Human Genetics 2008, 82:194-198. 10.1016/j.ajhg.2007.09.010, 2253960, 18179899.
40. Kimura R, Ohashi J, Matsumura Y, Nakazawa M, Inaoka T, Ohtsuka R, Osawa M, Tokunaga K. Gene flow and natural selection in oceanic human populations inferred from genome-wide SNP typing. Molecular Biology and Evolution 2008, 25:1750-1761. 10.1093/molbev/msn128, 18524786.
41. López Herráez D, Bauchet M, Tang K, Theunert C, Pugach I, Li J, Nandineni MR, Gross A, Scholz M, Stoneking M. Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS ONE 2009, 4:e7888. 2775638, 19924308.
42. Consortium TGP. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073. 10.1038/nature09534, 20981092.
43. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature 2010, 463:943-947. 10.1038/nature08795, 20164927.