Consistency of genome-wide associations across major ancestral groups

Human Genetics

Volumn 131, Issue 7, 2012, Pages 1057-1071

  Ntzani, Evangelia E ^a   Liberopoulos, George ^a   Manolio, Teri A ^b   Ioannidis, John P A ^a,c  

^a UNIVERSITY OF IOANNINA   (Greece)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; ASIAN; CAUCASIAN; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; GENE FREQUENCY; GENETIC ASSOCIATION; HUMAN; PRIORITY JOURNAL; RACE; RISK ASSESSMENT;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS;

EID: 84862775448     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-011-1124-4     Document Type: Article

References (53)

1. A Adeyemo C Rotimi 2010 Genetic variants associated with complex human diseases show wide variation across multiple populations Public Health Genomics 13 72 79 19439916 10.1159/000218711 1:STN:280:DC%2BD1MfhsVSqtQ%3D%3D
2. EA Ashley AJ Butte MT Wheeler R Chen TE Klein FE Dewey JT Dudley KE Ormond A Pavlovic AA Morgan, et al. 2010 Clinical assessment incorporating a personal genome Lancet 375 1525 1535 20435227 10.1016/S0140-6736(10)60452-7 1:CAS:528:DC%2BC3cXlsVOnt74%3D
3. W Bodmer C Bonilla 2008 Common and rare variants in multifactorial susceptibility to common diseases Nat Genet 40 695 701 18509313 10.1038/ng.f.136 1:CAS:528:DC%2BD1cXmsVejtrs%3D
4. K Bryc A Auton MR Nelson JR Oksenberg SL Hauser S Williams A Froment JM Bodo C Wambebe SA Tishkoff, et al. 2010 Genome-wide patterns of population structure and admixture in West Africans and African Americans Proc Natl Acad Sci USA 107 786 791 20080753 10.1073/pnas.0909559107 1:CAS:528: DC%2BC3cXhtFCmsL8%3D
5. EG Burchard E Ziv N Coyle SL Gomez H Tang AJ Karter JL Mountain EJ Pérez-Stable D Sheppard N Risch 2003 The importance of race and ethnic background in biomedical research and clinical practice N Engl J Med 348 1170 1175 12646676 10.1056/NEJMsb025007
6. CD Campbell EL Ogburn KL Lunetta HN Lyon ML Freedman LC Groop D Altshuler KG Ardlie JN Hirschhorn 2005 Demonstrating stratification in a European American population Nat Genet 37 868 872 16041375 10.1038/ng1607 1:CAS:528:DC%2BD2MXmsFKls7k%3D
7. JC Cappelleri JP Ioannidis CH Schmid SD de Ferranti M Aubert TC Chalmers J Lau 1996 Large trials vs meta-analysis of smaller trials: how do their results compare? JAMA 276 1332 1338 8861993 10.1001/jama.1996.03540160054033 1:STN:280:DyaK2s%2FhsFWltw%3D%3D
8. S Chinn 2000 A simple method for converting an odds ratio to effect size for use in meta-analysis Stat Med 19 3127 3131 11113947 10.1002/1097- 0258(20001130)19:22<3127::AID-SIM784>3.0.CO;2-M 1:STN:280: DC%2BD3MvjsVWguw%3D%3D
9. Cooper H, Hedges LV (eds) (1994) The handbook of research synthesis (Russell Sage 58. Foundation, New York)
10. R DerSimonian N Laird 1986 Meta-analysis in clinical trials Control Clin Tr 7 177 188 10.1016/0197-2456(86)90046-2 1:STN:280:DyaL2s7gsVamtA%3D%3D
11. PS Dhandapany S Sadayappan Y Xue GT Powell DS Rani P Nallari TS Rai M Khullar P Soares A Bahl, et al. 2009 A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia Nat Genet 41 187 191 19151713 10.1038/ng.309 1:CAS:528:DC%2BD1MXntFGrtQ%3D%3D
12. 1000 Genomes (2011) A deep catalog of human genetic variation. http://www.1000genomes.org/
13. SF Grant M Li JP Bradfield CE Kim K Annaiah E Santa JT Glessner T Casalunovo EC Frackelton FG Otieno, et al. 2008 Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP PLoS One 3 e1746 18335027 10.1371/journal.pone.0001746
14. J Gulcher K Stefansson 2010 Genetic risk information for common diseases may indeed be already useful for prevention and early detection Eur J Clin Invest 40 56 63 20055896 10.1111/j.1365-2362.2009.02233.x 1:STN:280: DC%2BC3c%2Fht1ertw%3D%3D
15. A Helgason S Pálsson G Thorleifsson SF Grant V Emilsson S Gunnarsdottir A Adeyemo Y Chen G Chen I Reynisdottir, et al. 2007 Refining the impact of TCF7L2 gene variants on type 2 diabetes and adaptive evolution Nat Genet 39 218 225 17206141 10.1038/ng1960 1:CAS:528:DC%2BD2sXpvFeqsA%3D%3D
16. JP Higgins SG Thompson JJ Deeks DG Altman 2003 Measuring inconsistency in meta-analyses BMJ 327 557 560 12958120 10.1136/bmj.327.7414.557
17. LA Hindorff P Sethupathy HA Junkins EM Ramos JP Mehta FS Collins TA Manolio 2009 Potential etiologic and functional implications of genome-wide association loci for human diseases and traits Proc Natl Acad Sci USA 106 9362 9367 19474294 10.1073/pnas.0903103106 1:CAS:528:DC%2BD1MXot1Cgur4%3D
18. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA (2011) A catalog of published genome-wide association studies. (Available at: http://www.genome.gov/gwastudies )
19. JP Ioannidis 2007 Non-replication and inconsistency in the genome-wide association setting Hum Hered 64 203 213 17551261 10.1159/000103512 1:CAS:528:DC%2BD2sXnslWrur4%3D
20. JP Ioannidis 2009 Population-wide generalizability of genome-wide discovered associations J Natl Cancer Inst 101 1297 1299 19726754 10.1093/jnci/djp298
21. JP Ioannidis 2009 Personalized genetic prediction: too limited, too expensive, or too soon? Ann Intern Med 150 139 141
22. JP Ioannidis EE Ntzani TA Trikalinos DG Contopoulos-Ioannidis 2001 Replication validity of genetic association studies Nat Genet 29 306 309 11600885 10.1038/ng749 1:CAS:528:DC%2BD3MXotlWgsLs%3D
23. JP Ioannidis EE Ntzani TA Trikalinos 2004 'Racial' differences in genetic effects for complex diseases Nat Genet 36 1312 1318 15543147 10.1038/ng1474 1:CAS:528:DC%2BD2cXhtVWitLvF
24. JP Ioannidis NA Patsopoulos E Evangelou 2007 Uncertainty in heterogeneity estimates in meta-analyses BMJ 335 914 916 17974687 10.1136/bmj.39343.408449.80
25. JP Ioannidis G Thomas MJ Daly 2009 Validating, augmenting and refining genome-wide association signals Nat Rev Genet 10 318 329 19373277 10.1038/nrg2544 1:CAS:528:DC%2BD1MXksF2rs7k%3D
26. AC Janssens CM van Duijn 2008 Genome-based prediction of common diseases: advances and prospects Hum Mol Genet 17 R166 R173 18852206 10.1093/hmg/ddn250 1:CAS:528:DC%2BD1cXhtlyjsrfK
27. H Li Y Wu RJ Loos FB Hu Y Liu J Wang Z Yu X Lin 2008 Variants in the fat mass- and obesity-associated (FTO) gene are not associated with obesity in a Chinese Han population Diabetes 57 264 268 17959933 10.2337/db07-1130 1:CAS:528:DC%2BD1cXmt1ajsQ%3D%3D
28. A Manica F Prugnolle F Balloux 2005 Geography is a better determinant of human genetic differentiation than ethnicity Hum Genet 118 366 371 16189711 10.1007/s00439-005-0039-3
29. N Mantel W Haenszel 1959 Statistical aspects of the analysis of data from retrospective studies of disease J Natl Cancer Inst 22 719 748 13655060 1:STN:280:DyaG1M%2FosVOhtQ%3D%3D
30. MI McCarthy GR Abecasis LR Cardon DB Goldstein J Little JP Ioannidis JN Hirschhorn 2008 Genome-wide association studies for complex traits: consensus, uncertainty and challenges Nat Rev Genet 9 356 369 18398418 10.1038/nrg2344 1:CAS:528:DC%2BD1cXkvVOhs7Y%3D
31. R Moonesinghe MJ Khoury T Liu JP Ioannidis 2008 Required sample size and nonreplicability thresholds for heterogeneous genetic associations Proc Natl Acad Sci USA 105 617 622 18174335 10.1073/pnas.0705554105 1:CAS:528: DC%2BD1cXpvV2rtQ%3D%3D
32. S Myers L Bottolo C Freeman G McVean P Donnelly 2005 A fine-scale map of recombination rates and hotspots across the human genome Science 310 321 324 16224025 10.1126/science.1117196 1:CAS:528:DC%2BD2MXhtV2hurvI
33. NCI-NHGRI Working Group on Replication in Association Studies SJ Chanock T Manolio M Boehnke E Boerwinkle DJ Hunter G Thomas JN Hirschhorn G Abecasis D Altshuler, et al. 2007 Replicating genotype-phenotype associations Nature 447 655 660 17554299 10.1038/447655a 1:CAS:528:DC%2BD2sXmtFemur4%3D
34. AC Need DB Goldstein 2006 Genome-wide tagging for everyone Nat Genet 38 1227 1228 17072295 10.1038/ng1106-1227 1:CAS:528:DC%2BD28XhtFeisbrI
35. MC Ng KS Park B Oh CH Tam YM Cho HD Shin VK Lam RC Ma WY So YS Cho, et al. 2008 Implication of genetic variants near TCF7L2, SLC30A8, HHEX, CDKAL1, CDKN2A/B, IGF2BP2, and FTO in type 2 diabetes and obesity in 6, 719 Asians Diabetes 57 2226 2233 18469204 10.2337/db07-1583 1:CAS:528:DC%2BD1cXps1OisLc%3D
36. TV Pereira NA Patsopoulos G Salanti JP Ioannidis 2009 Discovery properties of genome-wide association signals from cumulatively combined data sets Am J Epidemiol 170 1197 1206 19808636 10.1093/aje/kwp262
37. DF Ransohoff MJ Khoury 2010 Personal genomics: information can be harmful Eur J Clin Invest 40 64 68 20055897 10.1111/j.1365-2362.2009.02232.x 1:STN:280:DC%2BC3c%2Fht1ertA%3D%3D
38. NA Rosenberg L Huang EM Jewett ZA Szpiech I Jankovic M Boehnke 2010 Genome-wide association studies in diverse populations Nat Rev Genet 11 356 366 20395969 10.1038/nrg2760 1:CAS:528:DC%2BC3cXkvVSqs7w%3D
39. CD Royal J Novembre SM Fullerton DB Goldstein JC Long MJ Bamshad AG Clark 2010 Inferring genetic ancestry: opportunities, challenges, and implications Am J Hum Genet 86 661 673 20466090 10.1016/j.ajhg.2010.03.011 1:CAS:528: DC%2BC3cXms1arsLo%3D
40. RS Spielman LA Bastone JT Burdick M Morley WJ Ewens VG Cheung 2007 Common genetic variants account for differences in gene expression among ethnic groups Nat Genet 39 226 231 17206142 10.1038/ng1955 1:CAS:528:DC%2BD2sXpvFeruw%3D%3D
41. H Tang 2006 Confronting ethnicity-specific disease risk Nat Genet 38 13 15 16380723 10.1038/ng0106-13 1:CAS:528:DC%2BD2MXhtlCmtr7M
42. H Tang T Quertermous B Rodriguez SL Kardia X Zhu A Brown JS Pankow MA Province SC Hunt E Boerwinkle, et al. 2005 Genetic structure, self-identified race/ethnicity, and confounding in case-control association studies Am J Hum Genet 76 268 275 15625622 10.1086/427888 1:CAS:528:DC%2BD2MXpsFeisg%3D%3D
43. The International HapMap Project (2003) Nature 426:789-796
44. C Tian PK Gregersen MF Seldin 2008 Accounting for ancestry: population substructure and genome-wide association studies Hum Mol Genet 17 R143 R150 18852203 10.1093/hmg/ddn268 1:CAS:528:DC%2BD1cXhtlyjsrfP
45. SA Tishkoff FA Reed FR Friedlaender C Ehret A Ranciaro A Froment JB Hirbo AA Awomoyi JM Bodo O Doumbo, et al. 2009 The genetic structure and history of Africans and African Americans Science 324 1035 1044 19407144 10.1126/science.1172257 1:CAS:528:DC%2BD1MXmtVKlsbs%3D
46. BF Voight S Kudaravalli X Wen JK Pritchard 2006 A map of recent positive selection in the human genome PLoS Biol 4 e72 16494531 10.1371/journal.pbio. 0040072
47. KM Waters DO Stram MT Hassanein L Le Marchand LR Wilkens G Maskarinec KR Monroe LN Kolonel D Altshuler BE Henderson, et al. 2010 Consistent association of type 2 diabetes risk variants found in Europeans in diverse racial and ethnic groups PLoS Genet 6 e1001078 20865176 10.1371/journal.pgen.1001078
48. Wellcome Trust Case Control Consortium 2007 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 661 678 10.1038/nature05911
49. H Yamada KL Penney H Takahashi T Katoh Y Yamano M Yamakado T Kimura H Kuruma Y Kamata S Egawa, et al. 2009 Replication of prostate cancer risk loci in a Japanese case-control association study J Natl Cancer Inst 101 1330 1336 19726753 10.1093/jnci/djp287 1:CAS:528:DC%2BD1MXht1Ojt73P
50. JJ Yang EG Burchard S Choudhry CC Johnson DR Ownby D Favro J Chen M Akana C Ha PY Kwok, et al. 2008 Differences in allergic sensitization by self-reported race and genetic ancestry J Allergy Clin Immunol 122 820 827 19014772 10.1016/j.jaci.2008.07.044
51. Q Yang WD Flanders R Moonesinghe JP Ioannidis I Guessous MJ Khoury 2009 Using lifetime risk estimates in personal genomic profiles: estimation of uncertainty Am J Hum Genet 85 786 800 19931039 10.1016/j.ajhg.2009.10.017 1:CAS:528:DC%2BC3cXht1eqtrk%3D
52. W Zhang S Duan EO Kistner WK Bleibel RS Huang TA Clark TX Chen AC Schweitzer JE Blume NJ Cox, et al. 2008 Evaluation of genetic variation contributing to differences in gene expression between populations Am J Hum Genet 82 631 640 18313023 10.1016/j.ajhg.2007.12.015 1:CAS:528: DC%2BD1cXksVGrtb8%3D
53. S Zollner JK Pritchard 2007 Overcoming the winner's curse: estimating penetrance parameters from case-control data Am J Hum Genet 80 605 615 17357068 10.1086/512821 1:CAS:528:DC%2BD2sXktVOju7Y%3D