An assessment of the portability of ancestry informative markers between human populations

Sean Myles1, Mark Stoneking2, Nicholas J. Timpson3
1Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, 14853-2703, USA
2Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
3Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK

Tóm tắt

Từ khóa


Tài liệu tham khảo

Altshuler D, Daly MJ, Lander ES: Genetic Mapping in Human Disease. Science. 2008, 322 (5903): 881-888. 10.1126/science.1156409.

McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA, Hirschhorn JN: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008, 9 (5): 356-10.1038/nrg2344.

Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN: Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet. 2003, 33 (2): 177-10.1038/ng1071.

Knowler WC, Williams RC, Pettitt DJ, Steinberg AG: Gm3;5,13,14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am J Hum Genet. 1988, 43 (4): 520-526.

Bunker CH, Patrick AL, Konety BR, Dhir R, Brufsky AM, Vivas CA, Becich MJ, Trump DL, Kuller LH: High prevalence of screening-detected prostate cancer among Afro-Caribbeans: the Tobago Prostate Cancer Survey. Cancer Epidemiol Biomarkers Prev. 2002, 11 (8): 726-729.

Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, Adebamowo CA, Griffin R, Williams T, Ukoli F, Adams-Campbell L, et al: CYP3A4-V and prostate cancer in African Americans: causal or confounding association because of population stratification?. Hum Genet. 2002, 110 (6): 553-560. 10.1007/s00439-002-0731-5.

Tian C, Gregersen PK, Seldin MF: Accounting for ancestry: population substructure and genome-wide association studies. Hum Mol Genet. 2008, 17 (R2): R143-150. 10.1093/hmg/ddn268.

Pritchard JK, Stephens M, Rosenberg NA, Donnelly P: Association mapping in structured populations. Am J Hum Genet. 2000, 67 (1): 170-181. 10.1086/302959.

Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006, 38 (8): 904-909. 10.1038/ng1847.

Pritchard JK, Stephens M, Donnelly P: Inference of Population Structure Using Multilocus Genotype Data. Genetics. 2000, 155 (2): 945-959.

Hinds DA, Stokowski RP, Patil N, Konvicka K, Kershenobich D, Cox DR, Ballinger DG: Matching strategies for genetic association studies in structured populations. Am J Hum Genet. 2004, 74 (2): 317-325. 10.1086/381716.

Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, et al: Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat. 2008, 30 (1): 69-78. 10.1002/humu.20822.

Halder I, Shriver M, Thomas M, Fernandez JR, Frudakis T: A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. Hum Mutat. 2008, 29 (5): 648-658. 10.1002/humu.20695.

Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, Shigeta R, Silva G, Patel PI, Belmont JW, et al: Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet. 2005, 118 (3–4): 382-392. 10.1007/s00439-005-0012-1.

Enoch MA, Shen PH, Xu K, Hodgkinson C, Goldman D: Using ancestry-informative markers to define populations and detect population stratification. J Psychopharmacol. 2006, 20 (4 Suppl): 19-26. 10.1177/1359786806066041.

Lao O, Duijn Kv, Kersbergen P, Knijff Pd, Kayser M: Proportioning Whole-Genome Single-Nucleotide-Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry. Am J Hum Genet. 2006, 78 (4): 680-690. 10.1086/501531.

Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM: Control of confounding of genetic associations in stratified populations. Am J Hum Genet. 2003, 72 (6): 1492-1504. 10.1086/375613.

Heath SC, Gut IG, Brennan P, McKay JD, Bencko V, Fabianova E, Foretova L, Georges M, Janout V, Kabesch M, et al: Investigation of the fine structure of European populations with applications to disease association studies. Eur J Hum Genet. 2008, 16 (12): 1413-10.1038/ejhg.2008.210.

Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, et al: Genes mirror geography within Europe. Nature. 2008, 456 (7218): 98-10.1038/nature07331.

Lao O, Lu TT, Nothnagel M, Junge O, Freitag-Wolf S, Caliebe A, Balascakova M, Bertranpetit J, Bindoff LA, Comas D, et al: Correlation between Genetic and Geographic Structure in Europe. Curr Biol. 2008, 18 (16): 1241-10.1016/j.cub.2008.07.049.

Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, Selmi C, Klareskog L, Pulver AE, Qi L, Gregersen PK, et al: Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 2008, 4 (1): e4-10.1371/journal.pgen.0040004.

Price AL, Butler J, Patterson N, Capelli C, Pascali VL, Scarnicci F, Ruiz-Linares A, Groop L, Saetta AA, Korkolopoulou P, et al: Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. 2008, 4 (1): e236-10.1371/journal.pgen.0030236.

Bauchet M, McEvoy B, Pearson LN, Quillen EE, Sarkisian T, Hovhannesyan K, Deka R, Bradley DG, Shriver MD: Measuring European Population Stratification with Microarray Genotype Data. Am J Hum Genet. 2007, 80 (5): 948-10.1086/513477.

Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, Silva G, Belmont JW, Klareskog L, Gregersen PK: European Population Substructure: Clustering of Northern and Southern Populations. PLoS Genet. 2006, 2 (9): e143-10.1371/journal.pgen.0020143.

Paschou P, Drineas P, Lewis J, Nievergelt CM, Nickerson DA, Smith JD, Ridker PM, Chasman DI, Krauss RM, Ziv E: Tracing Sub-Structure in the European American Population with PCA-Informative Markers. PLoS Genet. 2008, 4 (7): e1000114-10.1371/journal.pgen.1000114.

Marchini J, Cardon LR, Phillips MS, Donnelly P: The effects of human population structure on large genetic association studies. Nat Genet. 2004, 36 (5): 512-517. 10.1038/ng1337.

Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, et al: Assessing the impact of population stratification on genetic association studies. Nat Genet. 2004, 36 (4): 388-393. 10.1038/ng1333.

Helgason A, Yngvadottir B, Hrafnkelsson B, Gulcher J, Stefansson K: An Icelandic example of the impact of population structure on association studies. Nat Genet. 2005, 37 (1): 90-95.

Jakkula E, Rehnström K, Varilo T, Pietiläinen OPH, Paunio T, Pedersen NL, deFaire U, Järvelin M-R, Saharinen J, Freimer N, et al: The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population. Am J Hum Genet. 2008, 83 (6): 787-10.1016/j.ajhg.2008.11.005.

Pfeufer A, Sanna S, Arking DE, Muller M, Gateva V, Fuchsberger C, Ehret GB, Orru M, Pattaro C, Kottgen A, et al: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. Nat Genet. 2009, 41 (4): 407-10.1038/ng.362.

Sulem P, Gudbjartsson DF, Stacey SN, Helgason A, Rafnar T, Magnusson KP, Manolescu A, Karason A, Palsson A, Thorleifsson G, et al: Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat Genet. 2007, 39 (12): 1443-1452. 10.1038/ng.2007.13.

Fujimoto A, Kimura R, Ohashi J, Omi K, Yuliwulandari R, Batubara L, Mustofa MS, Samakkarn U, Settheetham-Ishida W, Ishida T, et al: A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. Hum Mol Genet. 2008, 17 (6): 835-843. 10.1093/hmg/ddm355.

Fujimoto A, Ohashi J, Nishida N, Miyagawa T, Morishita Y, Tsunoda T, Kimura R, Tokunaga K: A replication study confirmed the EDAR gene to be a major contributor to population differentiation regarding head hair thickness in Asia. Hum Genet. 2008, 124 (2): 179-10.1007/s00439-008-0537-1.

Hu Y, Li L, Seidelmann SB, Timur AA, Shen PH, Driscoll DJ, Wang QK: Identification of Association of Common AGGF1 Variants with Susceptibility for Klippel-Trenaunay Syndrome Using the Structure Association Program. Ann Hum Genet. 2008, 72 (5): 636-643. 10.1111/j.1469-1809.2008.00458.x.

The Wellcome Trust Case Control Consortium: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007, 447 (7145): 661-678. 10.1038/nature05911.

Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A, et al: A human genome diversity cell line panel. Science. 2002, 296 (5566): 261-262. 10.1126/science.296.5566.261b.

Rosenberg NA: Standardized Subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, Accounting for Atypical and Duplicated Samples and Pairs of Close Relatives. Ann Hum Genet. 2006, 70 (6): 841-847. 10.1111/j.1469-1809.2006.00285.x.

KBiosciences: [ http://www.kbioscience.co.uk/genotyping/genotyping_chemistry.html ]

Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, et al: Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Science. 2008, 319 (5866): 1100-1104. 10.1126/science.1153717.

CEPH: [ http://www.cephb.fr/cephdb/ ]

Weir BS, Cockerham CC: Estimating F-statistics for the analysis of population structure. Evolution. 1984, 38: 1358-1370. 10.2307/2408641.

Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK: A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet. 2006, 38 (11): 1251-1260. 10.1038/ng1911.

Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW: Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure. PLoS Genet. 2005, 1 (6): e70-10.1371/journal.pgen.0010070.

Wright S: The theory of gene frequencies. 1969, Chicago: University of Chicago Press, 2.

Rosenberg NA, Li LM, Ward R, Pritchard JK: Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003, 73 (6): 1402-1422. 10.1086/380416.

Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M: Identification and analysis of high Fst regions from genome-wide SNP data from three human populations. Ann Hum Genet. 2008, 72 (1): 99-110.

Campbell CD, Ogburn EL, Lunetta KL, Lyon HN, Freedman ML, Groop LC, Altshuler D, Ardlie KG, Hirschhorn JN: Demonstrating stratification in a European American population. Nat Genet. 2005, 37 (8): 868-10.1038/ng1607.

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 Genet. 2007, 3 (9): e160-10.1371/journal.pgen.0030160.

Beaumont MA, Balding DJ: Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol. 2004, 13 (4): 969-980. 10.1111/j.1365-294X.2004.02125.x.

Pollinger JP, Bustamante CD, Fledel-Alon A, Schmutz S, Gray MM, Wayne RK: Selective sweep mapping of genes with large phenotypic effects. Genome Res. 2005, 15 (12): 1809-1819. 10.1101/gr.4374505.

Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN: Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet. 2004, 74 (6): 1111-1120. 10.1086/421051.