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Cited by 63Forensic and Genetic ResearchGenetic diversity and population structureRace, Genetics, and Society

Measurement of admixture proportions and description of admixture structure in different U.S. populations

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Halder, Indrani, Yang, Bao-Zhu, Kranzler, Henry R., Stein, Murray B., Shriver, Mark D., Gelernter, Joel·2009·Human Mutation
DOI 10.1002/humu.21045PMC PMC2867064
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Abstract

Variation in individual admixture proportions leads to heterogeneity within populations. Though novel methods and marker panels have been developed to quantify individual admixture, empirical data describing individual admixture distributions are limited. We investigated variation in individual admixture in four U.S. populations (European American [EA], African American [AA], Hispanics from Connecticut [East Coast, or EC], and Hispanics from California [West Coast, or WC]) assuming three-way intermixture among Europeans, Africans, and Indigenous Americans. Admixture estimates were inferred using a panel of 36 microsatellites and one SNP, which have significant allele frequency differences between ancestral populations, and by using both a maximum likelihood (ML)-based method and a Bayesian method implemented in the program STRUCTURE. Simulation studies showed that estimates obtained with this marker panel are within 96% of expected values. EAs had the lowest non-European admixture with both methods, but showed greater homogeneity with STRUCTURE than with ML. All other samples showed a high degree of variation in admixture estimates with both methods, were highly concordant, and showed evidence of admixture stratification. With both methods, AA subjects had on average, 16% European and <10% Indigenous American admixture. EC Hispanics had higher mean African admixture and the WC Hispanics had higher mean Indigenous American admixture, possibly reflecting their different continental origins.

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  • European Americans also have non-European ancestry, including African, Native American, and Asian, though it has been poorly quantified with some discordance among estimates even within studies.

    “Studies have shown that European Americans also have non-European ancestry, including African, Native American, and Asian, though it has been poorly quantified with some discordance among estimates even within studies.29–32”

    From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [30]

    The Results (Individual admixture proportions in US populations; page unavailable) report non-European admixture in some European Americans and significantly different estimates from the two methods. The paper analyzes European, African, and Indigenous American ancestry, but not Asian ancestry, so it does not support that part of the claim. (LLM, conf=0.90)

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  1. Bauchet M McEvoy B Pearson LN Quillen EE Sarkisian T Hovhannesyan K Deka R Bradley DG Shriver MD 2007 Measuring European population stratification with microarray genotype data Am J Hum Genet 80.5 948 56 17436249 PMC1852743
  2. Bertoni B Budowle B Sans M Barton SA Chakraborty R 2003 Admixture in Hispanics: distribution of ancestral population contributions in the Continental United States Hum Biol 75 1 11 12713142
  3. Bonilla C Parra EJ Pfaff CL Dios S Marshall JA Hamman RF Ferrell RE Hoggart CL McKeigue PM Shriver MD 2004 Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping Ann Hum Genet 68 139 153.a 15008793
  4. Bonilla C Shriver MD Parra EJ Jones A Fernandez JR 2004 Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York City Hum Genet 115 57 68.b 15118905
  5. Budowle B Shea B Niezgoda S Chakraborty R 2001 CODIS STR loci data from 41 sample populations J Forensic Sci 46 3 453 89 11372982
  6. Chakraborty R Weiss KM 1988 Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci Proc Natl Acad Sci U S A 85 9119 9123 3194414 PMC282675
  7. Collins-Schramm HE Chima B Morii T Wah K Figueroa Y Criswell LA Hanson RL Knowler WC Silva G Belmont JW Seldin MF 2004 Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians Hum Genet 114 263 271 14628215
  8. Collins-Schramm HE Phillips CM Operario DJ Lee JS Weber JL Hanson RL Knowler WC Cooper R Li H Seldin MF 2002 Ethnic-difference markers for use in mapping by admixture linkage disequilibrium Am J Hum Genet 70 737 750 11845411 PMC384950
  9. Devlin B Roeder K Wasserman L 2001 Genomic control, a new approach to genetic-based association studies Theor Popul Biol 60 155 166 11855950
  10. Douglas JG Thibonnier M Wright JT Jr 1996 Essential hypertension: racial/ethnic differences in pathophysiology J Assoc Acad Minor Phys 7 16 21 8820238
  11. Falush D Stephens M Pritchard JK 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies Genetics 164 1567 1587 12930761 PMC1462648
  12. Fernandez JR Shriver MD Beasley TM Rafla-Demetrious N Parra E Albu J Nicklas B Ryan AS McKeigue PM Hoggart CL Weinsier RL Allison DB 2003 Association of African genetic admixture with resting metabolic rate and obesity among women Obes Res 11 904 911 12855761
  13. Gardner LI Jr Stern MP Haffner SM Gaskill SP Hazuda HP Relethford JH Eifler CW 1984 Prevalence of diabetes in Mexican Americans. Relationship to percent of gene pool derived from Native American sources Diabetes 33 86 92 6690348
  14. Gresham D Morar B Underhill PA Passarino G Lin AA Wise C Angelicheva D Calafell F Oefner PJ Shen P Tournev I de Pablo R Kucinskas V Perez-Lezaun A Marushiakova E Popov V Kalaydjieva L 2001 Origins and divergence of the Roma gypsies Am J Hum Genet 69 1314 1331 11704928 PMC1235543
  15. Hanis CL Chakraborty R Ferrell RE Schull WJ 1986 Individual admixture estimates: disease associations and individual risk of diabetes and gallbladder disease among Mexican-Americans in Starr County, Texas Am J Phys Anthropol 70 433 441 3766713
  16. Heiman GA Hodge SE Gorroochurn P Zhang J Greenberg DA 2004 Effect of population stratification on case-control association studies. I. Elevation in false positive rates and comparison to confounding risk ratios. a simulation study Hum Hered 58 30 39 15604562
  17. Helgason A Sigureth ardottir S Nicholson J Sykes B Hill EW Bradley DG Bosnes V Gulcher JR Ward R Stefansson K 2000 Estimating Scandinavian and Gaelic ancestry in the male settlers of Iceland Am J Hum Genet 67 697 717 10931763 PMC1287529
  18. Hoffman RM Gilliland FD Eley JW Harlan LC Stephenson RA Stanford JL Albertson PC Hamilton AS Hunt WC Potosky AL 2001 Racial and ethnic differences in advanced-stage prostate cancer: the Prostate Cancer Outcomes Study J Natl Cancer Inst 93 388 395 11238701
  19. Hoffman RM Harlan LC Klabunde CN Gilliland FD Stephenson RA Hunt WC Potosky AL 2003 Racial differences in initial treatment for clinically localized prostate cancer. Results from the prostate cancer outcomes study J Gen Intern Med 18 845 853 14521648 PMC1494937
  20. Hoggart CJ Parra EJ Shriver MD Bonilla C Kittles RA Clayton DG McKeigue PM 2003 Control of confounding of genetic associations in stratified populations Am J Hum Genet 72 1492 1504 12817591 PMC1180309
  21. Kayser M Brauer S Schadlich H Prinz M Batzer MA Zimmerman PA Boatin BA Stoneking M 2003 Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry Genome Res 13 624 634 12671003 PMC430174
  22. Koller DL Peacock M Lai D Foroud T Econs MJ 2004 False positive rates in association studies as a function of degree of stratification J Bone Miner Res 19 1291 1295 15231016
  23. Kumar S Tamura K Jakobsen IB Nei M 2001 MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 1244 1245 11751241
  24. Long JC 1991 The genetic structure of admixed populations Genetics 127 417 428 2004712 PMC1204369
  25. Long JC Williams RC McAuley JE Medis R Partel R Tregellas WM South SF Rea AE McCormick SB Iwaniec U 1991 Genetic variation in Arizona Mexican Americans: estimation and interpretation of admixture proportions Am J Phys Anthropol 84 141 157 2021190
  26. Luo X Kranzler HR Zuo L Wang S Blumberg HP Gelernter J 2005 CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study Hum Mol Genet 14 16 2421 34 16000316
  27. Martinez NC 1993 Diabetes and minority populations. Focus on Mexican Americans Nurs Clin North Am 28 87 95 8451219
  28. McKeigue PM Carpenter JR Parra EJ Shriver MD 2000 Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations Ann Hum Genet 64 171 186 11246470
  29. Molokhia M Hoggart C Patrick AL Shriver M Parra E Ye J Silman AJ McKeigue PM 2003 Relation of risk of systemic lupus erythematosus to west African admixture in a Caribbean population Hum Genet 112 310 318 12545274
  30. Parra EJ Kittles RA Argyropoulos G Pfaff CL Hiester K Bonilla C Sylvester N Parrish-Gause D Garvey WT Jin L McKeigue PM Kamboh MI Ferrell RE Pollitzer WS Shriver MD 2001 Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina Am J Phys Anthropol 114 18 29 11150049
  31. Paschou P Drineas P Lewis J Nievergelt CM Nickerson DA Smith JD Ridker PM Chasman DI Krauss RM Ziv E 2008 Tracing sub-structure in the European American population with PCA-informative markers PLoS Genet 4;4 7 e1000114 PMC2537989 18797516
  32. Pfaff CL Parra EJ Bonilla C Hiester K McKeigue PM Kamboh MI Hutchinson RG Ferrell RE Boerwinkle E Shriver MD 2001 Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium Am J Hum Genet 68 198 207 11112661 PMC1234913
  33. Pritchard JK Donnelly P 2001 Case-control studies of association in structured or admixed populations Theor Popul Biol 60 227 237 11855957
  34. Pritchard JK Stephens M Donnelly P 2000 Inference of population structure using multilocus genotype data Genetics 155 945 959 10835412 PMC1461096
  35. Pritchard JK Stephens M Rosenberg NA Donnelly P 2000 Association mapping in structured populations Am J Hum Genet 67 170 181 10827107 PMC1287075
  36. Reiner AP Ziv E Lind DL Nievergelt CM Schork NJ Cummings SR Phong A Burchard EG Harris TB Psaty BM Kwok PY 2005 Population structure, admixture, and aging-related phenotypes in African American adults: the Cardiovascular Health Study Am J Hum Genet 76 463 477 15660291 PMC1196398
  37. Rosenberg NA Li LM Ward R Pritchard JK 2003 Informativeness of genetic markers for inference of ancestry Am J Hum Genet 73 1402 1422 14631557 PMC1180403
  38. Rousset F Raymond M 1995 Testing heterozygote excess and deficiency Genetics 140 1413 1419 7498780 PMC1206704
  39. Sans M 2000 Admixture studies in Latin America: from the 20th to the 21st century Hum Biol 72 155 177 10721616
  40. Shriver MD Mei R Parra EJ Sonpar V Halder I Tishkoff SA Schurr TG Zhadanov SI Osipova LP Brutsaert TD Friedlaender J Jorde LB Watkins WS Bamshad MJ Gutierrez G Loi H Matsuzaki H Kittles RA Argyropoulos G Fernandez JR Akey JM Jones KW 2005 Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation Hum Genomics 2 81 89 16004724 PMC3525270
  41. Shriver MD Parra EJ Dios S Bonilla C Norton H Jovel C Pfaff C Jones C Massac A Cameron N Baron A Jackson T Argyropoulos G Jin L Hoggart CJ McKeigue PM Kittles RA 2003 Skin pigmentation, biogeographical ancestry and admixture mapping Hum Genet 112 387 399 12579416
  42. Shriver MD Smith MW Jin L Marcini A Akey JM Deka R Ferrell RE 1997 Ethnic-affiliation estimation by use of population-specific DNA markers Am J Hum Genet 60 957 964 9106543 PMC1712479
  43. Smith MW Lautenberger JA Shin HD Chretien JP Shrestha S Gilbert DA O’Brien SJ 2001 Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations Am J Hum Genet 69 1080 1094 11590548 PMC1274377
  44. Songer TJ Zimmet PZ 1995 Epidemiology of type II diabetes: an international perspective Pharmacoeconomics 8 Suppl 1 1 11 10158995
  45. Stein MB Schork NJ Gelernter J 2004 A polymorphism of the beta1-adrenergic receptor is associated with low extraversion Biol Psychiatry 56 217 224 15312808
  46. Wang H Parry S Macones G Sammel MD Ferrand PE Kuivaniemi H Tromp G Halder I Shriver MD Romero R Strauss JF 3rd 2004 Functionally significant SNP MMP8 promoter haplotypes and preterm premature rupture of membranes Hum Mol Genet 13 2659 2669 15367487
  47. Wen B Xie X Gao S Li H Shi H Song X Qian T Xiao C Jin J Su B Lu D Chakraborty R Jin L 2004 Analyses of genetic structure of Tibeto-Burman populations reveals sex-biased admixture in southern Tibeto-Burmans Am J Hum Genet 74 856 865 15042512 PMC1181980
  48. Williams RC Knowler WC Pettitt DJ Long JC Rokala DA Polesky HF Hackenberg RA Steinberg AG Bennett PH 1992 The magnitude and origin of European-American admixture in the Gila River Indian Community of Arizona: a union of genetics and demography Am J Hum Genet 51 101 110 1609790 PMC1682879
  49. Yang BZ Zhao H Kranzler HR Gelernter J 2005 Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE Genet Epidemiol 28 302 312.a 15782414
  50. Yang BZ Zhao H Kranzler HR Gelernter J 2005 Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment BMC Genet 6 50.b 16225681 PMC1285360

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Authors
Halder, I., Yang, B.-Z., Kranzler, H. R., Stein, M. B., Shriver, M. D., & Gelernter, J.
Affiliations
  • Pennsylvania State University (US)
  • Yale University (US)
  • University of Connecticut (US)
  • University of California San Diego (US)
Corresponding author
Gelernter, Joel
ORCID
Venue
Human Mutation
Publisher
Hindawi Limited
Published
2009-09
Volume
30
Issue
9
Pages
1299-1309
ISSN
  • 1059-7794 (ISSN-L)
  • 1098-1004
DOI
10.1002/humu.21045
PMC
PMC2867064
OpenAlex
W2042006639
Cited by
63
References
3
Citations by year
2026: 1 · 2025: 2 · 2023: 1 · 2022: 1 · 2021: 3 · 2020: 1 · 2019: 6 · 2018: 4 · 2017: 2 · 2016: 6 · 2015: 4 · 2014: 9 · 2013: 2 · 2012: 7
FWCI
4.09
Type
journal article
Language
en
Open access
Licence
doi.wiley.com/10.1002/tdm_license_1.1 (tdm, 2191 d)
Locations
  • Human Mutation (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • U.S. Department of Veterans Affairs
  • National Institutes of Health
  • National Institute on Alcohol Abuse and Alcoholism (K24 AA13736, K24AA013736)
  • National Institute of Mental Health (MH-64122, K24MH064122)
  • National Institute on Drug Abuse (R01-DA12690, R01 DA 12849, K01DA024758, R01DA012690, R01DA012849)
  • National Center for Research Resources (M01RR006192, M01 RR 06192)
  • NIH Clinical Center
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
Keywords
European-American population, African American population, Hispanic population, microsatellite markers, structure, continental ancestry, United States population
MeSH terms
Black or African American, Gene Frequency, Genetic Markers, Genetics, Population, Genotype, Hispanic or Latino, Humans, Population Dynamics, Genetic Variation, Microsatellite Repeats, Black People, White People

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