Mapping of disease-associated variants in admixed populations

Genome Biology

Volumn 12, Issue 5, 2011, Pages

  Shriner, Daniel ^a   Adeyemo, Adebowale ^a   Ramos, Edward ^a   Chen, Guanjie ^a   Rotimi, Charles N ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; DISEASE PREDISPOSITION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC LINKAGE; GENETIC VARIABILITY; HISPANIC; HUMAN; POPULATION GENETICS; REVIEW; ALLELE; AMERICAN INDIAN; BIOLOGICAL MODEL; CARDIOVASCULAR DISEASE; CAUCASIAN; CHROMOSOME MAP; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; GENOMICS; METHODOLOGY; NEGRO; PHYLOGENY; POPULATION DYNAMICS; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; VIRUS INFECTION;

AFRICAN CONTINENTAL ANCESTRY GROUP; ALLELES; AMERICAN NATIVE CONTINENTAL ANCESTRY GROUP; CARDIOVASCULAR DISEASES; CHROMOSOME MAPPING; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENETICS, POPULATION; GENOMICS; HUMANS; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DYNAMICS; QUANTITATIVE TRAIT LOCI; VIRUS DISEASES;

EID: 79957616191     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-5-223     Document Type: Review

References (61)

1. Need AC, Goldstein DB. Next generation disparities in human genomics: concerns and remedies. Trends Genet 2009, 25:489-494. 10.1016/j.tig.2009.09.012, 19836853.
2. McCarthy MI. Casting a wider net for diabetes susceptibility genes. Nat Genet 2008, 40:1039-1040. 10.1038/ng0908-1039, 19165915.
3. Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat Rev Genet 2010, 11:356-366. 3079573, 20395969.
4. Rotimi CN, Jorde LB. Ancestry and disease in the age of genomic medicine. N Engl J Med 2010, 363:1551-1558. 10.1056/NEJMra0911564, 20942671.
5. Davey Smith G, Neaton JD, Wentworth D, Stamler R, Stamler J. Mortality differences between black and white men in the USA: contribution of income and other risk factors among men screened for the MRFIT. Lancet 1998, 351:934-939.
6. Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, Sulkowski M, McHutchison JG, Goldstein DB. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 2009, 461:399-401. 10.1038/nature08309, 19684573.
7. Winkler CA, Nelson GW, Smith MW. Admixture mapping comes of age. Annu Rev Genomics Hum Genet 2010, 11:65-89. 10.1146/annurev-genom-082509-141523, 20594047.
8. McKeigue PM. Prospects for admixture mapping of complex traits. Am J Hum Genet 2005, 76:1-7. 10.1086/426949, 1196412, 15540159.
9. Rife DC. Populations of hybrid origin as source material for the detection of linkage. Am J Hum Genet 1954, 6:26-33. 1716603, 13138567.
10. Chakraborty R, Weiss KM. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 1988, 85:9119-9123. 10.1073/pnas.85.23.9119, 282675, 3194414.
11. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly MJ, Reich D. Methods for high-density admixture mapping of disease genes. Am J Hum Genet 2004, 74:979-1000. 10.1086/420871, 1181990, 15088269.
12. 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, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, et al. A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 2004, 74:1001-1013. 10.1086/420856, 1181963, 15088270.
13. McKeigue PM. Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 1998, 63:241-251. 10.1086/301908, 1377232, 9634509.
14. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM. Design and analysis of admixture mapping studies. Am J Hum Genet 2004, 74:965-978. 10.1086/420855, 1181989, 15088268.
15. Montana G, Pritchard JK. Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 2004, 75:771-789. 10.1086/425281, 1182107, 15386213.
16. Price AL, Zaitlen NA, Reich D, Patterson N. New approaches to population stratification in genome-wide association studies. Nat Rev Genet 2010, 11:459-463. 2975875, 20548291.
17. Adeyemo A, Gerry N, Chen G, Herbert A, Doumatey A, Huang H, Zhou J, Lashley K, Chen Y, Christman M, Rotimi C. A genome-wide association study of hypertension and blood pressure in African Americans. PLoS Genet 2009, 5:e1000564. 10.1371/journal.pgen.1000564, 2702100, 19609347.
18. Chen G, Shriner D, Zhou J, Doumatey A, Huang H, Gerry NP, Herbert A, Christman MF, Chen Y, Dunston GM, Faruque MU, Rotimi CN, Adeyemo A. Development of admixture mapping panels for African Americans from commercial high-density SNP arrays. BMC Genomics 2010, 11:417. 10.1186/1471-2164-11-417, 2996945, 20602785.
19. The International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449:851-861. 10.1038/nature06258, 2689609, 17943122, The International HapMap Consortium.
20. Rieseberg LH, Whitton J, Gardner K. Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 1999, 152:713-727. 1460641, 10353912.
21. 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 Genet 2009, 5:e1000519. 10.1371/journal.pgen.1000519, 2689842, 19543370.
22. Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, Hammer M, Bustamante CD, Ostrer H. Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci USA 2010, 107(Suppl 2):8954-8961. 3024022, 20445096.
23. Via M, Gignoux CR, Roth LA, Fejerman L, Galanter J, Choudhry S, Toro-Labrador G, Viera-Vera J, Oleksyk TK, Beckman K, Ziv E, Risch N, Burchard EG, Martínez-Cruzado JC. History shaped the geographic distribution of genomic admixture on the island of Puerto Rico. PLoS ONE 2011, 6:e16513. 10.1371/journal.pone.0016513, 3031579, 21304981.
24. Akinbami LJ, Moorman JE, Liu X. Asthma prevalence, health care use, and mortality: United States, 2005-2009. Natl Health Stat Report 2011, 12:1-14.
25. Sha Q, Zhang X, Zhu X, Zhang S. Analytical correction for multiple testing in admixture mapping. Hum Hered 2006, 62:55-63. 10.1159/000096094, 17047335.
26. Zhu X, Zhang S, Tang H, Cooper R. A classical likelihood based approach for admixture mapping using EM algorithm. Hum Genet 2006, 120:431-445. 10.1007/s00439-006-0224-z, 16896924.
27. Nalls MA, Wilson JG, Patterson NJ, Tandon A, Zmuda JM, Huntsman S, Garcia M, Hu D, Li R, Beamer BA, Patel KV, Akylbekova EL, Files JC, Hardy CL, Buxbaum SG, Taylor HA, Reich D, Harris TB, Ziv E. Admixture mapping of white cell count: genetic locus responsible for lower white blood cell count in the Health ABC and Jackson Heart Studies. Am J Hum Genet 2008, 82:81-87. 10.1016/j.ajhg.2007.09.003, 2253985, 18179887.
28. Rosenberg NA, Nordborg M. A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations. Genetics 2006, 173:1665-1678. 10.1534/genetics.105.055335, 1526699, 16582435.
29. Epstein MP, Allen AS, Satten GA. A simple and improved correction for population stratification in case-control studies. Am J Hum Genet 2007, 80:921-930. 10.1086/516842, 1852732, 17436246.
30. Tiwari HK, Barnholtz-Sloan J, Wineinger N, Padilla MA, Vaughan LK, Allison DB. Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles. Hum Hered 2008, 66:67-86. 10.1159/000119107, 2803696,2803696, 18382087.
31. McClellan J, King MC. Why it is time to sequence. Cell 2010, 142:353-355.
32. Redden DT, Divers J, Vaughan LK, Tiwari HK, Beasley TM, Fernández JR, Kimberly RP, Feng R, Padilla MA, Liu N, Miller MB, Allison DB. Regional admixture mapping and structured association testing: conceptual unification and an extensible general linear model. PLoS Genet 2006, 2:e137. 10.1371/journal.pgen.0020137, 1557785, 16934005.
33. Qin H, Morris N, Kang SJ, Li M, Tayo B, Lyon H, Hirschhorn J, Cooper RS, Zhu X. Interrogating local population structure for fine mapping in genome-wide association studies. Bioinformatics 2010, 26:2961-2968. 10.1093/bioinformatics/btq560, 20889494.
34. Tang H, Siegmund DO, Johnson NA, Romieu I, London SJ. Joint testing of genotype and ancestry association in admixed families. Genetic Epidemiol 2010, 34:783-791.
35. Marchini J, Howie B. Genotype imputation for genome-wide association studies. Nat Rev Genet 2010, 11:499-511. 10.1038/nrg2796, 20517342.
36. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073. 10.1038/nature09534, 3042601, 20981092, The 1000 Genomes Project Consortium.
37. Paşaniuc B, Avinery R, Gur T, Skibola CF, Bracci PM, Halperin E. A generic coalescent-based framework for the selection of a reference panel for imputation. Genet Epidemiol 2010, 34:773-782. 10.1002/gepi.20505, 21058333.
38. Paşaniuc B, Sankararaman S, Kimmel G, Halperin E. Inference of locus-specific ancestry in closely related populations. Bioinformatics 2009, 25:i213-i221. 10.1093/bioinformatics/btp197, 2687951, 19477991.
39. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
40. Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardlie K, John EM, Oakley-Girvan I, Whittemore AS, Cooney KA, Ingles SA, Altshuler D, Henderson BE, Reich D. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc Natl Acad Sci USA 2006, 103:14068-14073. 10.1073/pnas.0605832103, 1599913, 16945910.
41. Amundadottir LT, Sulem P, Gudmundsson J, Helgason A, Baker A, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Cazier JB, Sainz J, Jakobsdottir M, Kostic J, Magnusdottir DN, Ghosh S, Agnarsson K, Birgisdottir B, Le RL, Olafsdottir A, Blondal T, Andresdottir M, Gretarsdottir OS, Bergthorsson JT, Gudbjartsson D, Gylfason A, Thorleifsson G, Manolescu A, Kristjansson K, Geirsson G, Isaksson H, Douglas J, et al. A common variant associated with prostate cancer in European and African populations. Nat Genet 2006, 38:652-658. 10.1038/ng1808, 16682969.
42. Gudmundsson J, Sulem P, Manolescu A, Amundadottir LT, Gudbjartsson D, Helgason A, Rafnar T, Bergthorsson JT, Agnarsson BA, Baker A, Sigurdsson A, Benediktsdottir KR, Jakobsdottir M, Xu J, Blondal T, Kostic J, Sun J, Ghosh S, Stacey SN, Mouy M, Saemundsdottir J, Backman VM, Kristjansson K, Tres A, Partin AW, Albers-Akkers MT, Godino-Ivan Marcos J, Walsh PC, Swinkels DW, Navarrete S, et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 2007, 39:631-637. 10.1038/ng1999, 17401366.
43. Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, Neubauer J, Tandon A, Schirmer C, McDonald GJ, Greenway SC, Stram DO, Le Marchand L, Kolonel LN, Frasco M, Wong D, Pooler LC, Ardlie K, Oakley-Girvan I, Whittemore AS, Cooney KA, John EM, Ingles SA, Altshuler D, Henderson BE, Reich D. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet 2007, 39:638-644. 10.1038/ng2015, 2638766, 17401364.
44. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, Minichiello MJ, Fearnhead P, Yu K, Chatterjee N, Wang Z, Welch R, Staats BJ, Calle EE, Feigelson HS, Thun MJ, Rodriguez C, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Giovannucci E, Willett WC, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Gelmann EP, Tucker M, Gerhard DS, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007, 39:645-649. 10.1038/ng2022, 17401363.
45. Haiman CA, Le Marchand L, Yamamato J, Stram DO, Sheng X, Kolonel LN, Wu AH, Reich D, Henderson BE. A common genetic risk factor for colorectal and prostate cancer. Nat Genet 2007, 39:954-956. 10.1038/ng2098, 2391283, 17618282.
46. Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, Yao K, Kehoe SM, Lenz HJ, Haiman CA, Yan C, Henderson BE, Frenkel B, Barretina J, Bass A, Tabernero J, Baselga J, Regan MM, Manak JR, Shivdasani R, Coetzee GA, Freedman ML. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet 2009, 41:882-884. 10.1038/ng.403, 2763485, 19561607.
47. Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, Yan C, Khalid O, Kantoff P, Oh W, Manak JR, Berman BP, Henderson BE, Frenkel B, Haiman CA, Freedman M, Tanay A, Coetzee GA. Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet 2009, 5:e1000597. 10.1371/journal.pgen.1000597, 2717370, 19680443.
48. Wasserman NF, Aneas I, Nobrega MA. An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome Res 2010, 20:1191-1197. 10.1101/gr.105361.110, 2928497, 20627891.
49. Ahmadiyeh N, Pomerantz MM, Grisanzio C, Herman P, Jia L, Almendro V, He HH, Brown M, Liu XS, Davis M, Caswell JL, Beckwith CA, Hills A, MacConaill L, Coetzee GA, Regan MM, Freedman ML. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci USA 2010, 107:9742-9746. 10.1073/pnas.0910668107, 2906844, 20453196.
50. Sotelo J, Esposito D, Duhagon MA, Banfield K, Mehalko J, Liao H, Stephens RM, Harris TJ, Munroe DJ, Wu X. Long-range enhancers on 8q24 regulate c-Myc. Proc Natl Acad Sci USA 2010, 107:3001-3005. 10.1073/pnas.0906067107, 2840341, 20133699.
51. Wright JB, Brown SJ, Cole MD. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol 2010, 30:1411-1420. 10.1128/MCB.01384-09, 2832500, 20065031.
52. Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2010, 42:579-589. 10.1038/ng.609, 3080658, 20581827.
53. Kopp JB, Smith MW, Nelson GW, Johnson RC, Freedman BI, Bowden DW, Oleksyk T, McKenzie LM, Kajiyama H, Ahuja TS, Berns JS, Briggs W, Cho ME, Dart RA, Kimmel PL, Korbet SM, Michel DM, Mokrzycki MH, Schelling JR, Simon E, Trachtman H, Vlahov D, Winkler CA. MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet 2008, 40:1175-1184. 10.1038/ng.226, 2827354, 18794856.
54. Kao WHL, Klag MJ, Meoni LA, Reich D, Berthier-Schaad Y, Li M, Coresh J, Patterson N, Tandon A, Powe NR, Fink NE, Sadler JH, Weir MR, Abboud HE, Adler SG, Divers J, Iyengar SK, Freedman BI, Kimmel PL, Knowler WC, Kohn OF, Kramp K, Leehey DJ, Nicholas SB, Pahl MV, Schelling JR, Sedor JR, Thornley-Brown D, Winkler CA, Smith MW, et al. MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet 2008, 40:1185-1192. 10.1038/ng.232, 2614692, 18794854.
55. The International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467:52-58. 10.1038/nature09298, 20811451, The International HapMap 3 Consortium.
56. Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ, Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak MR. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 2010, 329:841-845. 10.1126/science.1193032, 2980843, 20647424.
57. Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet 2006, 2:e190. 10.1371/journal.pgen.0020190, 1713260, 17194218.
58. Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK, Seldin MF. Analysis of East Asia genetic substructure using genome-wide SNP arrays. PLoS ONE 2008, 3:e3862. 10.1371/journal.pone.0003862, 2587696, 19057645.
59. Xu S, Jin L. A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. Am J Hum Genet 2008, 83:322-336. 10.1016/j.ajhg.2008.08.001, 2556439, 18760393.
60. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM. The genetic structure and history of Africans and African Americans. Science 2009, 324:1035-1044. 10.1126/science.1172257, 2947357, 19407144.
61. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH-Y, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, et al. A draft sequence of the Neandertal genome. Science 2010, 328:710-722. 10.1126/science.1188021, 20448178.