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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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“One hundred and six ancestry informative markers (AIMs) were used to control for population stratifi cation (i.e., race/ethnicity) (Halder et al., 2008; Hoggart et al., 2003; Tian et al., 2008).”
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“Finally, including Native American ancestral allele frequencies, as reported previously (16, 17, 26), might have yielded a more complete representation of the genetic diversity in these cohorts.”
BackgroundSelf-citationGenetic association of CD247 (CD3ζ) with SLE in a large-scale multiethnic study
Martins, M., Williams, A. H., Comeau, M. E., Marion, M. C., Ziegler, J. T., Freedman, B. I., Merrill, J. T., Glenn, S. B., Kelly, J. A., Sivils, K. L. M., et al. (2015) · Genes and Immunity · doi:10.1038/gene.2014.73 · Cited by 28
“The AIMs were selected to distinguish four continental ancestral populations: Africans, Europeans, American Indians, and East Asians.41,42 Principal components from EIGENSTRAT outputs were used to identify genetic outliers from each population cluster (as described in Lessard et al.37).”
Bülbül, Ö., Cherni, L., Khodjet‐El‐Khil, H., Rajeevan, H., & Kídd, K. K. (2016) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2016.04.010 · Cited by 28
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“Numerous human genetic markers have been suggested for inferring human genetic ancestry mostly to the continental level [4–7], and a recent study indicated that inferring the subregion of origin of an unknown European may be feasible from autosomal genetic data [8].”
BackgroundPrediction of biogeographical ancestry in admixed individuals
Cheung, E. Y. Y., Gahan, M. E., & McNevin, D. B. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.06.013 · Cited by 27
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“AIMs are used to minimize bias due to population substructure (Halder et al., 2008; Hoggart et al., 2003; Tian et al., 2008).”
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Moriot, A., Santos, C., Freire-Aradas, A., Phillips, C., & Hall, D. (2018) · European Journal of Human Genetics · doi:10.1038/s41431-018-0215-2 · Cited by 25
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“We also screened the HapMap database (the International HapMap Consortium 2003) and literature data associated with AIMs [25–28].”
MethodPhillips, A. E., LaRusch, J., Greer, P. J., Abberbock, J. N., Alkaade, S., Amann, S. T., Anderson, M. A., Baillie, J. M., Banks, P. A., Brand, R. E., et al. (2018) · Pancreatology · doi:10.1016/j.pan.2018.05.482 · Cited by 22
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Background- Applications of Autosomal SNPs and Indels in Forensic Analysis
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Getachew, T., Huson, H. J., Wurzinger, M., Burgstaller, J. P., Gizaw, S., Haile, A., Rischkowsky, B., Brem, G., Boison, S. A., Mészáros, G., et al. (2017) · BMC Genetics · doi:10.1186/s12863-017-0526-2 · Cited by 22
“96 reported for different human populations in prediction of admixture level using selected AIMs [28].”
BackgroundMethodApplication of machine learning for ancestry inference using multi-InDel markers
Sun, K., Yao, Y., Yun, L., Zhang, C., Xie, J., Qian, X., Tang, Q., & Sun, L. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102702 · Cited by 20
A genome wide pattern of population structure and admixture in peninsular Malaysia Malays
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AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels
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Annotating individual human genomes
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“With enough genetic markers across the genome that exhibit frequency differences across populations (‘Ancestry Informative Markers’) estimates of an individual’s ancestry can be made [82].”
BackgroundBarbosa, F. B., Cagnin, N. F., Simioni, M., de Farias, A. A., Torres, F. R., Molck, M. C., de Araujo, T. K., Gil‐da‐Silva‐Lopes, V. L., Donadi, E. A., & Simões, A. L. (2017) · Annals of Human Genetics · doi:10.1111/ahg.12208 · Cited by 20
“…(i.e., common variants in the general population) allowed the identification of 345 AIMs, previously reported as suitable to distinguish between European, African and Amerindian populations (Shriver et al., 2003; Halder et al., 2008; Kosoy et al., 2009; Lins et al., 2010; Galanter et al., 2012).”
BackgroundMethodInfluentialWide Disparity in Genetic Admixture Among Mexican Americans from San Antonio, TX
Beuten, J., Halder, I., Fowler, S. P., Göring, H. H. H., Duggirala, R., Arya, R., Thompson, I. M., Leach, R. J., & Lehman, D. M. (2011) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2011.00655.x · Cited by 20
“Halder et al. (2008) and Bonilla et al. (2004b) also found an association between skin pigmentation and Native American ancestry, although such correlation was not observed in other studies (Marshall et al., 1993; Bonilla et al., 2004a).”
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Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource
Bradbury, C., Köttgen, A., & Staubach, F. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.10.010 · Cited by 22
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“A subset of these AIMs is described elsewhere.(44) These markers were chosen because they exhibit large frequency differences between ancestral West African, Amerindian and West European populations.”
BackgroundPilli, E., Morelli, S., Poggiali, B., & Alladio, E. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102806 · Cited by 18
Forensic DNA phenotyping: a review on SNP panels, genotyping techniques, and prediction models
Terrado-Ortuño, N., & May, P. (2024) · Forensic Sciences Research · doi:10.1093/fsr/owae013 · Cited by 19
“As observed, some physical characteristics, in particular pigmentation traits, vary according to continental populations [8, 11, 66, 80].”
Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies
Dziech, A. (2021) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2021.760160 · Cited by 17
Cleveland, H. H., Griffin, A. M., Wolf, P. S. A., Wiebe, R. P., Schlomer, G. L., Feinberg, M. E., Greenberg, M. T., Spoth, R. L., Redmond, C. R., & Vandenbergh, D. J. (2017) · Prevention Science · doi:10.1007/s11121-017-0749-5 · Cited by 18
Differential Susceptibility: The Genetic Moderation of Peer Pressure on Alcohol Use
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“To assess and control for population stratification, this study used principal coordinates analysis (PCoA; Halder et al. 2008).”
Genetic Admixture and Obesity: Recent Perspectives and Future Applications
Fernández, J. R., Pearson, K. E., Kell, K. P., & Brown, M. M. B. (2013) · Human Heredity · doi:10.1159/000353180 · Cited by 17
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“These results are particularly relevant for the inclusion of African American data in forensic, anthropological and pharmacogenetic studies [64–67].”
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Vandenbergh, D. J., Schlomer, G. L., Cleveland, H. H., Schink, A. E., Hair, K. L., Feinberg, M. E., Neiderhiser, J. M., Greenberg, M. T., Spoth, R. L., & Redmond, C. R. (2015) · Nicotine & Tobacco Research · doi:10.1093/ntr/ntv095 · Cited by 15
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Genetic ancestry, skin color and social attainment: The four cities study
Teteh, D., Dawkins-Moultin, L., Hooker, S. E., Hernandez, W., Bonilla, C., Galloway, D., LaGroon, V., Santos, E. R., Shriver, M. D., Royal, C. D. M., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0237041 · Cited by 15
Self-citationAssociations of Obesity Genes with Obesity-related Outcomes in Multiethnic Children
Klimentidis, Y. C., Chen, G., López‐Alarcón, M., Harris, J. J., Duarte, C. W., & Fernández, J. R. (2011) · Archives of Medical Research · doi:10.1016/j.arcmed.2011.07.003 · Cited by 15
“Genetic Admixture Analysis A total of 142 ancestry informative markers (AIMs) were genotyped for each subject by Prevention Genetics (Mashfield, WI) as described elsewhere (17).”
MethodMiaskowski, C. A., Elboim, C., Paul, S. M., Mastick, J., Cooper, B. A., Levine, J. D., & Aouizerat, B. E. (2014) · Clinical Breast Cancer · doi:10.1016/j.clbc.2014.12.001 · Cited by 15
“Ancestry informative markers (AIMs) were used to minimize confounding due to population stratification.(51-53) The homogeneity in ancestry among the patients was verified by principal component analysis(54) using HelixTree (GoldenHelix, Bozeman, MT).”
MethodDeep Learning Approach to Biogeographical Ancestry Inference
Qu, Y., Tran, D., & Ma, W. (2019) · Procedia Computer Science · doi:10.1016/j.procs.2019.09.210 · Cited by 14
“The loci where exhibit extreme allele frequency di ff erences between populations are often counted as ancestry informative markers (AIMs) [49, 23] or the ancestry-sensitive markers [27] to describe the uncertainties.”
BackgroundMethodHajiloo, M., Sapkota, Y., Mackey, J. R., Robson, P. J., Greiner, R., & Damaraju, S. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-61 · Cited by 14
“A small set (typically tens to hundreds) of well-established AIMs can perfectly distinguish continental differences between individuals [13-16]; however, panels of AIMs, described thus far, are less informative in detecting sub-continental differences in closely related populations such as Europeans [17-25].”
BackgroundDNA fingerprinting in anthropological genetics: past, present, future
Crawford, M. H., & Beaty, K. G. (2013) · Investigative Genetics · doi:10.1186/2041-2223-4-23 · Cited by 13
Zhao, J., Giles, B. M., Taylor, R. L., Yette, G. A., Lough, K. M., Ng, H. L., Abraham, L. J., Wu, H. M., Kelly, J. A., Glenn, S. B., et al. (2014) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2014-205584 · Cited by 14
Alexander, K. E., Conley, Y. P., Levine, J. D., Cooper, B. A., Paul, S. M., Mastick, J., West, C. M., & Miaskowski, C. A. (2017) · Journal of Pain and Symptom Management · doi:10.1016/j.jpainsymman.2017.09.020 · Cited by 14
Paech, G. M., Crowley, S. J., Fogg, L., & Eastman, C. I. (2017) · PLoS ONE · doi:10.1371/journal.pone.0186887 · Cited by 12
A systematic review of gene-by-intervention studies of alcohol and other substance use
Neale, Z. E., Kuo, S. I., & Dick, D. M. (2020) · Development and Psychopathology · doi:10.1017/s0954579420000590 · Cited by 15
Iris texture traits show associations with iris color and genomic ancestry
Quillen, E. E., Guiltinan, J., Beleza, S. S., Rocha, J., Pereira, R. W., & Shriver, M. D. (2011) · American Journal of Human Biology · doi:10.1002/ajhb.21183 · Cited by 13
“AMERICAN JOURNAL OF HUMAN BIOLOGY 23:567–569 (2011) VC 2011 Wiley-Liss, Inc. markers (AIMs, Halder et al., 2008).”
BackgroundSelf-citationOlcha, M., Franasiak, J. M., Shastri, S. M., Molinaro, T. A., Congdon, H., Treff, N. R., & Scott, R. T. (2016) · Fertility and Sterility · doi:10.1016/j.fertnstert.2016.03.052 · Cited by 13
Estimating Genetic Ancestry Proportions from Faces
Klimentidis, Y. C., & Shriver, M. D. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004460 · Cited by 14
“These estimates rely on allele frequencies of AIMs in four putative un-admixed parental populations [39].”
MethodSelf-citationRe-conceptualizing Associations between Race and Morbidities of Extreme Prematurity
Burris, H. H., Hwang, S. S., Collins, J. W., Kirpalani, H. M., & Wright, C. J. (2019) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2018.12.052 · Cited by 12
Biochip for genotyping SNPs defining core Y-chromosome haplogroups in Russian population groups
Fesenko, D. O., Alexander, C., Sergey, S., Tatyana, N., & Alexander, Z. (2014) · BioChip Journal · doi:10.1007/s13206-014-8303-z · Cited by 12
Cytokine polymorphisms are associated with daytime napping in adults living with HIV
Byun, E., Gay, C., Portillo, C. J., Pullinger, C. R., Aouizerat, B. E., & Lee, K. A. (2017) · Sleep Medicine · doi:10.1016/j.sleep.2016.12.021 · Cited by 12
(WIHS), A. F. T. W. I. H. S., Baxi, S. M., Greenblatt, R. M., Bacchetti, P., Cohen, M. H., DeHovitz, J. A., Anastos, K., Gange, S. J., Young, M., & Aouizerat, B. E. (2017) · The Pharmacogenomics Journal · doi:10.1038/tpj.2017.3 · Cited by 12
Spector, S. A., Brummel, S. S., Nievergelt, C. M., Maihofer, A. X., Singh, K. K., Purswani, M. U., Williams, P. L., Hazra, R., Dyke, R. V., & Seage, G. R. (2016) · Medicine · doi:10.1097/md.0000000000004733 · Cited by 10
“[7–12] In addition, the use of race/ethnicity to define individual background is without generally agreed-upon definitions and have been called flawed surrogates for genetic factors in disease causation.”
BackgroundPalmer, O. M. P., Rogers, G. L., Yende, S. P., Angus, D. C., Clermont, G., & Langston, M. A. (2017) · Shock · doi:10.1097/shk.0000000000001029 · Cited by 11
“Since Black Americans in the United States are an admixed population, meaning they are of both African and European ancestry, we genotyped all the Black patients in our study cohort for 93 ancestry informative markers as previously described (18).”
Maróti, Z., Boldogkői, Z., Tombácz, D., Snyder, M. P., & Kalmár, T. (2018) · BMC Genomics · doi:10.1186/s12864-018-5168-x · Cited by 11
Yang, H., Wang, P., Lin, C., Chen, C.-H., & Chen, C. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-346 · Cited by 11
“more detailed understanding of the genetic background of study populations [2,4,5,7,13,14].”
BackgroundInfluentialAlexander, K. E., Cooper, B. A., Paul, S. M., Yates, P. M., Aouizerat, B. E., & Miaskowski, C. A. (2016) · Quality of Life Research · doi:10.1007/s11136-016-1310-x · Cited by 11
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Non-Hodgkin Lymphoma Risk and Variants in Genes Controlling Lymphocyte Development
Schuetz, J. M., Daley, D., Leach, S. R., Conde, L., Berry, B. R., Gallagher, R. P., Connors, J. M., Gascoyne, R. D., Bracci, P. M., Skibola, C. F., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075170 · Cited by 10
A Small Number of Candidate Gene SNPs Reveal Continental Ancestry in African Americans
Kodaman, N., Aldrich, M. C., Smith, J. R., Signorello, L. B., Bradley, K., Breyer, J. P., Cohen, S. S., Long, J., Cai, Q., Giles, J., et al. (2012) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2012.00738.x · Cited by 10
“…markers for this purpose are termed Ancestry Informative Markers (AIMs), which are selected for their large allele frequency differences between ancestral populations (Shriver et al., 1997; Akey et al., 2002; Rosenberg et al., 2003; Smith et al., 2004; Halder et al., 2008; Nassir et al., 2009; ).”
BackgroundJin, X., Cui, W., Chen, C., Guo, Y., Tao, Y., Lan, Q., Kong, T., & Zhu, B. (2019) · Electrophoresis · doi:10.1002/elps.201900241 · Cited by 10
Biyocoğrafik Soy Tahmini ve Adli Bilimlerde Kullanımı
Bülbül, Ö., & Filoğlu, G. (2019) · The Bulletin of Legal Medicine · doi:10.17986/blm.2019250174 · Cited by 10
Wilson, R. T., Roff, A. N., Dai, P. J., Fortugno, T., Douds, J. J., Chen, G., Grove, G. L., Nikiforova, S. O., Barnholtz‐Sloan, J. S., Frudakis, T. N., et al. (2011) · Hormone Molecular Biology and Clinical Investigation · doi:10.1515/hmbci.2011.021 · Cited by 8
“[27] This panel excludes the two skin pigmentation SNPs of interest in our study (i.”
BackgroundSelf-citationAn assessment of the portability of ancestry informative markers between human populations
Myles, S., Stoneking, M., & Timpson, N. J. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-45 · Cited by 8
Genetic predictors for bacterial vaginosis in women living with and at risk for HIV infection
Murphy, K., Shi, Q., Hoover, D. R., Adimora, A. A., Alcaide, M. L., Brockmann, S., Daubert, E. M., Duggal, P., Merenstein, D. J., Dionne, J. A., et al. (2024) · American Journal of Reproductive Immunology · doi:10.1111/aji.13845 · Cited by 6
Das, R., & Upadhyai, P. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy182 · Cited by 7
Toma, T. T., Dawson, J. M., & Adjeroh, D. (2018) · BMC Medical Genomics · doi:10.1186/s12920-018-0412-4 · Cited by 7
Prestes, P. R., Mitchell, R. J., Daniel, R., Sánchez, J. J., & van Oorschot, R. A. H. (2015) · Australian Journal of Forensic Sciences · doi:10.1080/00450618.2015.1022600 · Cited by 7
“Individuals declared as European were assigned to hgs H (25), U (16), T (7), J (6), V (4) or K (1), each considered a European lineage and only rarely seen outside the region(35).”
MethodYu, J., Taylor, J. S., Edwards, K. L., & Fullerton, S. M. (2012) · AJOB Primary Research · doi:10.1080/21507716.2012.717339 · Cited by 7
“The analytical advantages of ancestry estimation are most often touted by those who develop AIMs and ancestry estimation methods (Halder et al. 2008; Nassir et al. 2009).”
BackgroundA Bioinformatics Crash Course for Interpreting Genomics Data
Rotroff, D. M. (2020) · CHEST Journal · doi:10.1016/j.chest.2020.03.004 · Cited by 7
Merriman, J. D., Aouizerat, B. E., Cataldo, J. K., Dunn, L. B., Kober, K. M., Langford, D. J., West, C. M., Cooper, B. A., Paul, S. M., & Miaskowski, C. A. (2014) · European Journal of Oncology Nursing · doi:10.1016/j.ejon.2014.11.004 · Cited by 7
“Selfreported race/ethnicity and three principal components derived from one hundred six ancestry informative markers (AIMs) were controlled for in these analyses to minimize confounding due to population stratification (Halder et al., 2008; Hoggart et al., 2003; Tian et al., 2008).”
MethodLevels of Genital Tract Defensins and Cytokines Differ between HIV ‐Uninfected US and African Women
Murphy, K., Richardson, B. A., Dezzutti, C. S., Marrazzo, J. M., Hillier, S. L., Hendrix, C. W., & Herold, B. C. (2015) · American Journal of Reproductive Immunology · doi:10.1111/aji.12411 · Cited by 7
Rodrigues, M. L. D. B., Rodrigues, M. P., Norton, H., Mendes‐Junior, C. T., Simões, A. L., & Lawson, D. J. (2024) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2024.103153 · Cited by 8
What can one chromosome tell us about human biogeographical ancestry?
Toma, T. T., Williams, Z. D., Dawson, J. M., & Adjeroh, D. (2017) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2017.8217648 · Cited by 6
“Although a small set (typically few hundreds) of SNPs can distinguish continental differences between individuals using the Fst feature [13-14]; such panels of SNPs are less informative in detecting sub-continental differences in closely related populations [3, 15].”
Background
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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