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A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications
Open accessAbstract
Autosomal ancestry informative markers (AIMs) are useful for inferring individual biogeographical ancestry (I-BGA) and admixture. Ancestry estimates obtained from Y and mtDNA are useful for reconstructing population expansions and migrations in our recent past but individual genomic admixture estimates are useful to test for association of admixture with phenotypes, as covariate in association studies to control for stratification and, in forensics, to estimate certain overt phenotypes from ancestry. We have developed a panel of 176 autosomal AIMs that can effectively distinguish I-BGA and admixture proportions from four continental ancestral populations: Europeans, West Africans, Indigenous Americans, and East Asians. We present allele frequencies for these AIMs in all four ancestral populations and use them to assess the global apportionment of I-BGA and admixture diversity among some extant populations. We observed patterns of apportionment similar to those described previously using sex and autosomal markers, such as European admixture for African Americans (14.3%) and Mexicans (43.2%), European (65.5%) and East Asian affiliation (27%) for South Asians, and low levels of African admixture (2.8-10.8%) mirroring the distribution of Y E3b haplogroups among various Eurasian populations. Using simulation studies and pedigree analysis we show that I-BGA estimates obtained using this panel and a four-population model has a high degree of precision (average root mean square error [RMSE]=0.026). Using ancestry-phenotype associations we demonstrate that a large and informative AIM panel such as this can help reduce false-positive and false-negative associations between phenotypes and admixture proportions, which may result when using a smaller panel of less informative AIMs.
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“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 [29]
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Citations
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Inference of Population Structure Using Multilocus Genotype Data
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Interrogating a high-density SNP map for signatures of natural selection.Preprint
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Self-citationThe phylogeography of Y chromosome binary haplotypes and the origins of modern human populations
Underhill, P. A., Passarino, G., Lin, A. A., Shen, P., Lahr, M. M., Foley, R., Oefner, P. J., & Cavalli-Sforza, L. L. (2001) · Annals of Human Genetics · doi:10.1046/j.1469-1809.2001.6510043.x · Cited by 782
Estimating African American Admixture Proportions by Use of Population-Specific Alleles
Parra, E. J., Marcini, A., Akey, J., Martinson, J., Batzer, M. A., Cooper, R., Forrester, T., Allison, D. B., Deka, R., Ferrell, R. E., et al. (1998) · The American Journal of Human Genetics · doi:10.1086/302148 · Cited by 771 · cited 2×
“This report builds upon previously published AIM panels suitable for I-BGA and admixture analysis on a continental level [Shriver et al., 1997, 2003; Parra et al., 1998; Collins-Schramm et al., 2002; Bonilla et al., 2004a, b; Smith et al., 2004; Yang et al., 2005], but, is significantly larger and more accurate, and i…”
MethodSelf-citationLarge-scale genotyping of complex DNA
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Skin pigmentation, biogeographical ancestry and admixture mapping
Shriver, M. D., Parra, E. J., Dios, S., Bonilla, C., Norton, H., Jovel, C., Pfaff, C., Jones, C., Massac, A., Cameron, N., et al. (2003) · Human Genetics · doi:10.1007/s00439-002-0896-y · Cited by 549
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Cited by
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The genetic ancestry of African Americans, Latinos, and European Americans across the United States
Bryc, K., Durand, E. Y., Macpherson, J. M., Reich, D., & Mountain, J. L. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.11.010 · Cited by 712
An overview of STRUCTURE: applications, parameter settings, and supporting software
Porras-Hurtado, L., Ruíz, Y., Santos, C., Phillips, C., Carracedo, Á., & Lareu, M. V. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00098 · Cited by 646
for UK Primary Sjögren's Syndrome Registry, Lessard, C. J., Li, H., Adrianto, I., Ice, J. A., Rasmussen, A., Grundahl, K. M., Kelly, J. A., Dozmorov, M. G., Miceli‐Richard, C., et al. (2013) · Nature Genetics · doi:10.1038/ng.2792 · Cited by 542
Accounting for ancestry: population substructure and genome-wide association studies
Tian, C., Gregersen, P. K., & Seldin, M. F. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn268 · Cited by 375
“First, a small number of AIMs can be used to provide continental ancestry information (35,39,40).”
BackgroundSantos, N., Ribeiro-Rodrigues, E., Ribeiro-dos-Santos, Â., Pereira, R., Gusmão, L., Amorim, A., Guerreiro, J. F., Zago, M., Matte, C., Hutz, M., et al. (2010) · Human Mutation · doi:10.1002/humu.21159 · Cited by 324
“In most studies, these AIMs consisted of single-nucleotide polymorphisms (SNPs) [BennTorres et al., 2008; Choudhry et al., 2006; Kosoy et al., 2009; Parra et al., 1998, 2001; Shriver et al., 2003], but insertion-deletion polymorphisms (INDELs) of small DNA fragments [Bedoya et al., 2006] and short tandem repeats [Pime…”
ResultInfluential
Metadata
- Authors
- Halder, I., Shriver, M., Thomas, M., Fernandez, J. R., & Frudakis, T.
- Affiliations
- Pennsylvania State University (US)
- Corresponding author
- Halder, Indrani
- ORCID
- Shriver, Mark
- Venue
- Human Mutation
- Publisher
- Hindawi Limited
- Published
- 2008-02-19
- Volume
- 29
- Issue
- 5
- Pages
- 648-658
- ISSN
- 1059-7794 (ISSN-L)
- OpenAlex
- W2006535221
- Cited by
- 274
- References
- 44
- Citations by year
- 2026: 9 · 2025: 2 · 2024: 13 · 2023: 7 · 2022: 8 · 2021: 6 · 2020: 7 · 2019: 15 · 2018: 20 · 2017: 19 · 2016: 20 · 2015: 25 · 2014: 30 · 2013: 27 · 2012: 20
- FWCI
- 8.57
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute on Aging (P30AG015294)
- National Human Genome Research Institute
- 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
- Social Sciences › Anthropology › Race, Genetics, and Society
- Keywords
- ancestry informative markers, autosomal markers, allele frequency, European ancestry, West African ancestry, Indigenous American ancestry, East Asian ancestry
- MeSH terms
- Alleles, DNA, Female, Gene Frequency, Genetics, Population, Genotype, Humans, Male, Pedigree, Polymorphism, Single Nucleotide, Population Groups
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