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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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“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…”
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“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
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ResultInfluentialForensically Relevant SNP Classes
Budowle, B., & van Daal, A. (2008) · BioTechniques · doi:10.2144/000112806 · Cited by 298
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Modeling 3D Facial Shape from DNA
Claes, P., Liberton, D. K., Daniels, K., Rosana, K. M., Quillen, E. E., Pearson, L. N., McEvoy, B., Bauchet, M., Zaidi, A. A., Yao, W., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004224 · Cited by 202
“These transformations can be visualized with the texture map as well as shape only, and the GUI (http:// tinyurl.com/DNA2FACEIN3D) allows for the illustration of the comparison of transformed faces to the consensus face using the three primary FSCPs.”
BackgroundMethodInfluentialSelf-citationAssociation of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus
Adrianto, I., Wen, F., Templeton, A., Wiley, G., King, J. B., Lessard, C. J., Bates, J. S., Hu, Y., Kelly, J. A., Kaufman, K. M., et al. (2011) · Nature Genetics · doi:10.1038/ng.766 · Cited by 279
“Genotyping was performed on the Illumina iSelect platform at OMRF for 127 SNPs (chromosome 6 at 138,001,148–138,295,172 bp; NCBI build 36, dbSNP build 126) and 347 genome-wide AIM”
MethodMicrotia‐anotia: A global review of prevalence rates
Luquetti, D. V., Leoncini, E., & Mastroiacovo, P. (2011) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.20836 · Cited by 222
“…confirmed that this group represents a continuous along the Europeans and Indigenous Americans axes, and that the term “Hispanic” shows little correspondence with genetic ancestry or even ancestral admixture since not all Hispanics exhibit substantial Native American ancestry (Halder et al., 2008).”
BackgroundInferring genetic ancestry: Opportunities, challenges, and implications
Royal, C. D., Novembre, J., Fullerton, S. M., Goldstein, D. B., Long, J. C., Bamshad, M. J., & Clark, A. G. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.03.011 · Cited by 271
Lessard, C. J., Adrianto, I., Ice, J. A., Wiley, G. B., Kelly, J. A., Glenn, S. B., Adler, A. J., Li, H., Rasmussen, A., Williams, A. H., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.02.023 · Cited by 183
Nassir, R., Kosoy, R., Tian, C., White, P. A., Butler, L. M., Silva, G. O., Kittles, R. A., Alarcón-Riquelme, M. E., Gregersen, P. K., Belmont, J. W., et al. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-39 · Cited by 184
“As we and others have previously discussed, ancestry informative markers (AIMs) can be used as a tool to minimize bias due to population stratification in case-control association studies [ 1-4 ].”
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“Ancestry informative markers (AIMs) can be used as a tool to minimize confounding due to population stratification in case-control association studies [82–84].”
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Doong, S.-H., Dhruva, A., Dunn, L. B., West, C. M., Paul, S. M., Cooper, B. A., Elboim, C., Abrams, G., Merriman, J. D., Langford, D. J., et al. (2014) · Biological Research For Nursing · doi:10.1177/1099800414550394 · Cited by 170
Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set
Phillips, C., Parson, W., Lundsberg, B., Santos, C., Freire-Aradas, A., Torres, M. L., Eduardoff, M., Børsting, C., Johansen, P., Fondevila, M., et al. (2014) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2014.02.012 · Cited by 153
“[19]; 128 of the American population analysis panel of Kosoy et al.”
A Risk Variant in an miR-125b Binding Site in BMPR1B Is Associated with Breast Cancer Pathogenesis
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“Recently, AIMs useful for determining intercontinental admixture have been described to facilitate structured association testing in case-control studies (27).”
BackgroundFondevila, M., Phillips, C., Santos, C., Freire-Aradas, A., Vallone, P. M., Butler, J. M., Lareu, M. V., & Carracedo, Á. (2012) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2012.06.007 · Cited by 134
“In fact during this period two other SNP typing chemistries have been discontinued: a chip-based system used in a multiple-reaction ancestry test that typed 176 SNPs [14] (Beckman-Coulter GenomeLab SNPstream(1)) and an oligo-ligation system: AB Genplex(1), that held much promise for a range of forensic SNP typing appl…”
MethodPhenotypic associations of genetic susceptibility loci in systemic lupus erythematosus
Sánchez, E., Nadig, A., Richardson, B. C., Freedman, B. I., Kaufman, K. M., Kelly, J. A., Niewold, T. B., Kamen, D. L., Gilkeson, G. S., Ziegler, J. T., et al. (2011) · Annals of the Rheumatic Diseases · doi:10.1136/ard.2011.154104 · Cited by 128
Livestock Genomics for Developing Countries – African Examples in Practice
Marshall, K., Gibson, J. P., Mwai, O. A., Mwacharo, J. M., Haile, A., Getachew, T., Mrode, R., & Kemp, S. J. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00297 · Cited by 128
Sánchez, E., Comeau, M. E., Freedman, B. I., Kelly, J. A., Kaufman, K. M., Langefeld, C. D., Brown, E. E., Alarcón, G. S., Kimberly, R. P., Edberg, J. C., et al. (2011) · Arthritis & Rheumatism · doi:10.1002/art.30563 · Cited by 120
The Ethnic/Racial Variations of Intracerebral Hemorrhage (ERICH) Study Protocol
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“21 We will use existing software such as Structure 22 and Admixmap 23, 24 to compute individual admixture proportion.”
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Lai, C., Tucker, K. L., Choudhry, S., Parnell, L. D., Mattei, J., García‐Bailo, B., Beckman, K. B., Burchard, E. G., & Ordovás, J. M. (2008) · Human Genetics · doi:10.1007/s00439-008-0612-7 · Cited by 111
“[PubMed: 11512677] Martínez-Cruzado JC, Toro-Labrador G, Viera-Vera J, Rivera-Vega MY, Startek J, Latorre-Esteves M, Román-Colón A, Rivera-Torres R, Navarro-Millán IY, Gómez-Sánchez E, Caro-González HY, Valencia-Rivera P. Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis.”
InfluentialEastman, C., Suh, C., Tomaka, V. A., & Crowley, S. (2015) · Scientific Reports · doi:10.1038/srep08381 · Cited by 97
Miaskowski, C. A., Dodd, M. J., Paul, S. M., West, C. M., Hamolsky, D., Abrams, G., Cooper, B. A., Elboim, C., Neuhaus, J. M., Schmidt, B. L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060164 · Cited by 102
“Ancestry informative markers (AIMS) were used to minimize confounding due to population stratification [35–37].”
MethodPereira, V., Mogensen, H. S., Børsting, C., & Morling, N. (2017) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2017.02.013 · Cited by 95
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“The AIMs were selected to distinguish four continental ancestral populations: Africans, Europeans, American Indians, and East Asians (Figure 1).(10,11) We utilized principal components from EIGENSTRAT outputs to identify outliers from each population cluster.”
MethodKottyan, L. C., Zoller, E. E., Bene, J., Lu, X., Kelly, J. A., Rupert, A., Lessard, C. J., Vaughn, S. E., Marion, M. C., Weirauch, M. T., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu455 · Cited by 84
“We used 347 ancestral informative markers (AIMs) from the same custom genotyping study that passed quality control in both EIGENSTRAT (64) and ADMIXMAP (59,61) to distinguish the four continental ancestral populations, allowing identification of the substructure within the sample set (62,65).”
MethodGenetics and genomics in Brazil: a promising future
Passos‐Bueno, M. R., Bertola, D. R., Horovitz, D. D. G., Ferraz, V. E. D. F., & Brito, L. A. (2014) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.95 · Cited by 83
“Accordingly, AIMs have proven to be useful for inferring the putative biogeographic ancestry of individuals, estimating the ancestry proportions of admixed individuals and populations (Shriver et al. 1997; Halder et al. 2008; Pena et al. 2011; Pereira et al. 2012; Suarez-Kurtz et al. 2012; Manta et al. 2013), correcti…”
BackgroundLi, H., Reksten, T. R., Ice, J. A., Kelly, J. A., Adrianto, I., Rasmussen, A., Wang, S., He, B., Grundahl, K. M., Glenn, S. B., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006820 · Cited by 84
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Association of two independent functional risk haplotypes in TNIP1 with systemic lupus erythematosus
Adrianto, I., Wang, S., Wiley, G. B., Lessard, C. J., Kelly, J. A., Adler, A. J., Glenn, S. B., Williams, A. H., Ziegler, J. T., Comeau, M. E., et al. (2012) · Arthritis & Rheumatism · doi:10.1002/art.34642 · Cited by 80
ABIN1 Dysfunction as a Genetic Basis for Lupus Nephritis
Caster, D. J., Korte, E. A., Nanda, S. K., McLeish, K. R., Oliver, R. K., G'Sell, R. T., Sheehan, R. M., Freeman, D. W., Coventry, S. C., Kelly, J. A., et al. (2013) · Journal of the American Society of Nephrology · doi:10.1681/asn.2013020148 · Cited by 78
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Multilocus OCA2 genotypes specify human iris colors
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Self-citationRole of MYH9 and APOL1 in African and non-African populations with lupus nephritis
Lin, C. P., Adrianto, I., Lessard, C. J., Kelly, J. A., Kaufman, K. M., Guthridge, J. M., Freedman, B. I., Anaya, J., Alarcón-Riquelme, M. E., Networks, O. B. O. T. B. A. G., et al. (2011) · Genes and Immunity · doi:10.1038/gene.2011.82 · Cited by 72
A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia
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“Numerous panels of ancestry informative markers (AIMs) using SNPs or insertiondeletion marker have been published [7–15].”
BackgroundMiaskowski, C. A., Cooper, B. A., Dhruva, A., Dunn, L. B., Langford, D. J., Cataldo, J. K., Baggott, C., Merriman, J. D., Dodd, M. J., Lee, K. A., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040560 · Cited by 70
“Ancestry informative markers (AIMs) can be used as a tool to minimize confounding due to population stratification in casecontrol association studies [66–68].”
MethodPacifiplex : an ancestry-informative SNP panel centred on Australia and the Pacific region
Santos, C., Phillips, C., Fondevila, M., Daniel, R., van Oorschot, R. A. H., Burchard, E. G., Schanfield, M. S., Souto, L., Uacyisrael, J., Vía, M., et al. (2015) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2015.10.003 · Cited by 72
“Therefore, forensic analysis has adopted a range of autosomal SNP sets that can be used as a stand-alone tool or to provide additional ancestry data complementary to uniparental variation [11,14,16–21].”
BackgroundMAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations
Phillips, C., McNevin, D. B., Kídd, K. K., Lagace, R. E., Wootton, S., de la Puente, M., Freire-Aradas, A., Mosquera‐Miguel, A., Eduardoff, M., Gross, T. E., et al. (2019) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2019.06.022 · Cited by 69
Leung, G., Baggott, C., West, C. M., Elboim, C., Paul, S. M., Cooper, B. A., Abrams, G., Dhruva, A., Schmidt, B. L., Kober, K. M., et al. (2014) · Lymphatic Research and Biology · doi:10.1089/lrb.2013.0024 · Cited by 70
“Ancestry informative markers (AIMS) were used to minimize confounding due to population stratification.(33-35) Homogeneity in ancestry among patients was verified by principal component”
Guo, G., Fu, Y., Lee, H. E., Cai, T., Harris, K. M., & Li, Y. (2013) · Demography · doi:10.1007/s13524-013-0242-0 · Cited by 73
“…(and thus potential AIMs), while Europeans had 580 such SNPs. Rosenberg et al. (2002) found that 100–160 SNPs were sufficient when the sample size was roughly 1,000; other studies have generally used 150–200, with samples of at least 400 (Halder et al. 2008; Smith et al. 2001; Yang et al. 2005).”
Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers
Algee-Hewitt, B. F. B., Edge, M. D., Kim, J., Li, J. Z., & Rosenberg, N. A. (2016) · Current Biology · doi:10.1016/j.cub.2016.01.065 · Cited by 68
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“Ancestry-Informative Markers (AIMs) presenting marked allele frequency differentials between geographically separated groups have proven to be especially useful for inferring the putative biogeographic origin of individuals and estimate the ancestry proportions of admixed individuals and populations (e.g. Shriver et a…”
BackgroundAmbers, A., Churchill, J. D., King, J. L., Stoljarova, M., Gill-King, H., Assidi, M., Abu-Elmagd, M. M., Buhmeida, A. S., & Budowle, B. (2016) · BMC Genomics · doi:10.1186/s12864-016-3087-2 · Cited by 67
Stephens, K., Cooper, B. A., West, C. M., Paul, S. M., Baggott, C., Merriman, J. D., Dhruva, A., Kober, K. M., Langford, D. J., Leutwyler, H. C., et al. (2013) · Journal of Pain · doi:10.1016/j.jpain.2013.09.015 · Cited by 67
Assessment of the Precision ID Ancestry panel
Al-Asfi, M., McNevin, D. B., Mehta, B., Power, D., Gahan, M. E., & Daniel, R. (2018) · International Journal of Legal Medicine · doi:10.1007/s00414-018-1785-9 · Cited by 64
A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus
Wang, S., Adrianto, I., Wiley, G. B., Lessard, C. J., Kelly, J. A., Adler, A. J., Glenn, S. B., Williams, A. H., Ziegler, J. T., Comeau, M. E., et al. (2012) · Genes and Immunity · doi:10.1038/gene.2012.6 · Cited by 62
Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans
Kersbergen, P., van Duijn, K., Kloosterman, A., den Dunnen, J. T., Kayser, M., & de Knijff, P. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-69 · Cited by 65
“Other groups have also identified sets of ASMs that could differentiate the major geographical regions [39, 40 ].”
BackgroundThe GenoChip: A New Tool for Genetic Anthropology
Elhaik, E., Greenspan, E., Staats, S., Krahn, T., Tyler‐Smith, C., Xue, Y., Tofanelli, S., Francalacci, P., Cucca, F., Pagani, L., et al. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt066 · Cited by 59
Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas
Stefflova, K., Dulik, M., Barnholtz-Sloan, J., Pai, A., Walker, A., & Rebbeck, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014495 · Cited by 70
“1%, Senegalese/ Nigerians ,95%), and the admixture profile resembles that of other African American groups in the US [47], [48] (79–83%).”
Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening
Shraga, R., Yarnall, S., Elango, S., Manoharan, A. P., Rodriguez, S. A., Bristow, S. L., Kumar, N., Niknazar, M., Hoffman, D. I., Ghadir, S., et al. (2017) · BMC Genetics · doi:10.1186/s12863-017-0570-y · Cited by 59
Creary, L. E., Gangavarapu, S., Mallempati, K. C., Montero-Martín, G., Caillier, S. J., Santaniello, A., Hollenbach, J. A., Oksenberg, J. R., & Fernández-Viña, M. (2019) · Human Immunology · doi:10.1016/j.humimm.2019.07.275 · Cited by 59
Gandhi, M., Greenblatt, R. M., Bacchetti, P., Jin, C., Huang, Y., Anastos, K., Cohen, M. H., DeHovitz, J. A., Sharp, G. B., Gange, S. J., et al. (2012) · The Journal of Infectious Diseases · doi:10.1093/infdis/jis508 · Cited by 58
“Ancestry informative markers (AIMs) were used to estimate ancestry and as a tool to minimize bias due to population stratification [26].”
MethodDunn, L. B., Aouizerat, B. E., Langford, D. J., Cooper, B. A., Dhruva, A., Cataldo, J. K., Baggott, C., Merriman, J. D., Dodd, M. J., West, C. M., et al. (2012) · European Journal of Oncology Nursing · doi:10.1016/j.ejon.2012.10.004 · Cited by 58
“Ancestry informative markers (AIMS) were used to minimize confounding due to population stratification (Halder et al., 2008; Hoggart et al., 2003; Tian et al., 2008).”
MethodKeating, B. J., Bansal, A. T., Walsh, S., Millman, J. S., Newman, J., Kídd, K. K., Budowle, B., Eisenberg, A. J., Donfack, J., Gasparini, P., et al. (2012) · International Journal of Legal Medicine · doi:10.1007/s00414-012-0788-1 · Cited by 58
“Autosomal AIM sets usually provide ancestry resolution at the level of broad geographic regions such as continents [21–25], whereas with some particular Ychromosomal and mitochondrial AIMs, within-continental Z.”
Halder, I., Marsland, A. L., Cheong, J., Muldoon, M. F., Ferrell, R. E., & Manuck, S. B. (2009) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2009.09.014 · Cited by 57
“…in African Americans than European Americans (Carlson et al., 2005; Lange et al., 2006), further research is warranted, using African American samples implement- ing appropriate controls for genetic admixture using ancestry informative markers (e.g. Halder and Shriver, 2003; Halder et al., 2008).”
Self-citationTrans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4
Manku, H., Langefeld, C. D., Guerra, S. G., Malik, T. H., Alarcón-Riquelme, M. E., Anaya, J., Bae, S., Boackle, S. A., Brown, E. E., Criswell, L. A., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003554 · Cited by 55
“We also genotyped 347 SNPs used by Halder [29] to correct for major ancestry in each population as identified by a PCA-based approach (Supplementary Figure S1).”
MethodKober, K. M., Smoot, B. J., Paul, S. M., Cooper, B. A., Levine, J. D., & Miaskowski, C. A. (2016) · Journal of Pain and Symptom Management · doi:10.1016/j.jpainsymman.2016.04.014 · Cited by 56
Halder, I., Yang, B.-Z., Kranzler, H. R., Stein, M. B., Shriver, M. D., & Gelernter, J. (2009) · Human Mutation · doi:10.1002/humu.21045 · Cited by 63
“These populations may, depending on the particular group sampled, have very different individual admixture proportions [Halder et al., 2008].”
BackgroundMethodInfluentialSelf-citationEastman, C., Tomaka, V. A., & Crowley, S. (2016) · Scientific Reports · doi:10.1038/srep36716 · Cited by 48
Genetic ancestry plays a central role in population pharmacogenomics
Yang, H., Chen, C., Lin, Y., & Chu, S. (2021) · Communications Biology · doi:10.1038/s42003-021-01681-6 · Cited by 51
Dhruva, A., Aouizerat, B. E., Cooper, B. A., Paul, S. M., Dodd, M. J., West, C. M., Wara, W., Lee, K. A., Dunn, L. B., Langford, D. J., et al. (2014) · Biological Research For Nursing · doi:10.1177/1099800414534313 · Cited by 52
Improving ancestry distinctions among Southwest Asian populations
Bülbül, Ö., Speed, W. C., Gürkan, C., Soundararajan, U., Rajeevan, H., PAKSTIS, A. J., & Kídd, K. K. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.03.010 · Cited by 51
Langford, D. J., Paul, S. M., West, C. M., Dunn, L. B., Levine, J. D., Kober, K. M., Dodd, M. J., Miaskowski, C. A., & Aouizerat, B. E. (2015) · Pain · doi:10.1097/01.j.pain.0000460319.87643.11 · Cited by 49
“Ancestry informative markers can be used to minimize confounding due to population stratification.(19,22,64) Homogeneity in ancestry among patients was verified by principal component analysis,(49) using Helix Tree (Golden Helix, Bozeman, MT).”
MethodEshragh, J. L., Dhruva, A., Paul, S. M., Cooper, B. A., Mastick, J., Hamolsky, D., Levine, J. D., Miaskowski, C. A., & Kober, K. M. (2016) · Journal of Pain and Symptom Management · doi:10.1016/j.jpainsymman.2016.08.004 · Cited by 48
Soundararajan, U., Yun, L., Shi, M., & Kídd, K. K. (2016) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2016.01.013 · Cited by 47
“m [30].”
BackgroundStephens, K., Levine, J. D., Aouizerat, B. E., Paul, S. M., Abrams, G., Conley, Y. P., & Miaskowski, C. A. (2017) · Cytokine · doi:10.1016/j.cyto.2017.07.006 · Cited by 47
Wei, Y., Wei, L., Zhao, L., Sun, Q.-F., Jiang, L., Zhang, T., Liu, H.-B., Chen, J., Ye, J., Hu, L., et al. (2015) · International Journal of Legal Medicine · doi:10.1007/s00414-015-1183-5 · Cited by 44
“We assembled 968 of the most informative SNPs for inferring continental ancestries and predicting pigment phenotypes from a variety of sources, including 11 previous described panels respectively containing 56 [2], 176 [20], 47 [4], 128 [5], 446 [8], 35 [3, 13], 23 [14], and 35 [15] ancestryinformative SNPs, as well a…”
MethodRacial and Ethnic Health Disparities in Reproductive Medicine: An Evidence-Based Overview
Owen, C. M., Goldstein, E. H., Clayton, J. A., & Segars, J. H. (2013) · Seminars in Reproductive Medicine · doi:10.1055/s-0033-1348889 · Cited by 45
Impact of Genetic Ancestry on Outcomes in ECOG-ACRIN-5103
Schneider, B. P., Shen, F., Jiang, G., O’Neill, A., Radovich, M., Li, L., Gardner, L., Lai, D., Foroud, T., Sparano, J. A., et al. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00059 · Cited by 43
CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins
Londin, E. R., Keller, M., Maista, C., Smith, G., Mamounas, L. A., Zhang, R., Madore, S. J., Gwinn, K. A., & Corriveau, R. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013443 · Cited by 41
“100) to determine continental ancestry have been described [16,21,22,54].”
BackgroundTan, W., Sunahori, K., Zhao, J., Deng, Y., Kaufman, K. M., Kelly, J. A., Langefeld, C. D., Williams, A. H., Comeau, M. E., Ziegler, J. T., et al. (2011) · Arthritis & Rheumatism · doi:10.1002/art.30452 · Cited by 42
Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation
Lee, S., Kasif, S., Weng, Z., & Cantor, C. R. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003906 · Cited by 42
“A recent study indicates that most populations do not satisfy this criterion[32].”
Aouizerat, B. E., Dhruva, A., Paul, S. M., Cooper, B. A., Kober, K. M., & Miaskowski, C. A. (2015) · Journal of Pain and Symptom Management · doi:10.1016/j.jpainsymman.2015.05.008 · Cited by 41
“Ancestry informative markers (AIMs) were used to minimize confounding because of population stratification.(54,55) Homogeneity in ancestry among participants was verified by principal component analysis(56)”
Lee, K. A., Gay, C., Pullinger, C. R., Koenig, M. D., Zak, R., & Aouizerat, B. E. (2014) · SLEEP · doi:10.5665/sleep.3474 · Cited by 39
Gay, C., Zak, R., Lerdal, A., Pullinger, C. R., Aouizerat, B. E., & Lee, K. A. (2014) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2014.11.018 · Cited by 40
Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
Lu, X., Zoller, E. E., Weirauch, M. T., Wu, Z., Namjou, B., Williams, A. H., Ziegler, J. T., Comeau, M. E., Marion, M. C., Glenn, S. B., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.03.002 · Cited by 40
African Genetic Ancestry is Associated with Sleep Depth in Older African Americans
Halder, I., Matthews, K. A., Buysse, D. J., Strollo, P. J., Causer, V., Reís, S. E., & Hall, M. H. (2015) · SLEEP · doi:10.5665/sleep.4888 · Cited by 40
Self-citationGenetic Vulnerability to Menthol Cigarette Preference in Women
Oncken, C. A., Feinn, R., Covault, J., Duffy, V. B., Dornelas, E. A., Kranzler, H. R., & Sankey, H. Z. (2015) · Nicotine & Tobacco Research · doi:10.1093/ntr/ntv042 · Cited by 40
Merriman, J. D., Aouizerat, B. E., Cataldo, J. K., Dunn, L. B., Cooper, B. A., West, C. M., Paul, S. M., Baggott, C., Dhruva, A., Kober, K. M., et al. (2013) · Cytokine · doi:10.1016/j.cyto.2013.11.003 · Cited by 40
Lee, S., Epstein, M. P., Duncan, R., & Lin, X. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21621 · Cited by 40
“…samples with known population structure (like the International HapMap project) and select as AIMs those SNPs that show the most between-population variation in allele frequencies [Smith et al., 2004; Lao et al., 2006; Tian et al., 2006; Kosoy et al., 2008; Price et al., 2008; Halder et al., 2008].”
BackgroundCytokine polymorphisms are associated with fatigue in adults living with HIV/AIDS
Lee, K. A., Gay, C., Lerdal, A., Pullinger, C. R., & Aouizerat, B. E. (2014) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2014.02.017 · Cited by 39
“Ancestry informative markers (AIMs) are used to minimize bias due to population substructure (Halder et al., 2008; Hoggart et al., 2003; Tian et al., 2008).”
Stefflova, K., Dulik, M. C., Pai, A. A., Walker, A. H., Zeigler-Johnson, C. M., Gueye, S. M. K., Schurr, T. G., & Rebbeck, T. R. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007842 · Cited by 39
“2%, respectively, in the US [41]), as well as our own autosomal estimates from a subset of the samples (95.”
BackgroundChaitanya, L., van Oven, M., Weiler, N., Harteveld, J., Wirken, L., Sijen, T., de Knijff, P., & Kayser, M. (2014) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2014.02.010 · Cited by 37
“Although sets of ancestryinformative autosomal SNPs have been suggested recently [4–7], the resolution at which biogeographic origin can be obtained with these SNP sets does not reach even the continental level, as geographic regions in close proximity such as Europe, Western and Central Asia and Northern Africa are u…”
BackgroundEvaluating the accuracy of AIM panels at quantifying genome ancestry
Pardo‐Seco, J., Martinón‐Torres, F., & Salas, A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-543 · Cited by 40
“[37] refer to 170 AIMs; however, their supplementary data file refers to 176 AIMs.”
BackgroundCleveland, H. H., Schlomer, G. L., Vandenbergh, D. J., Feinberg, M. E., Greenberg, M. T., Spoth, R. L., Redmond, C. R., Shriver, M. D., Zaidi, A. A., & Hair, K. L. (2015) · Development and Psychopathology · doi:10.1017/s0954579414001291 · Cited by 37
Self-citationSingle Nucleotide Polymorphisms and Applications
Butler, J. M. (2011) · Elsevier eBooks · doi:10.1016/b978-0-12-374513-2.00012-9 · Cited by 43
A plausibly causal functional lupus-associated risk variant in the STAT1–STAT4 locus
Patel, Z. H., Lu, X., Miller, D., Forney, C. R., Lee, J., Lynch, A., Schroeder, C., Parks, L. G., Magnusen, A. F., Chen, X., et al. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy140 · Cited by 37
Wright, F., Hammer, M. J., Paul, S. M., Aouizerat, B. E., Kober, K. M., Conley, Y. P., Cooper, B. A., Dunn, L. B., Levine, J. D., Melkus, G. D., et al. (2017) · Cytokine · doi:10.1016/j.cyto.2016.12.023 · Cited by 36
Alfaro, E., Dhruva, A., Langford, D. J., Koetters, T., Merriman, J. D., West, C. M., Dunn, L. B., Paul, S. M., Cooper, B. A., Cataldo, J. K., et al. (2013) · European Journal of Oncology Nursing · doi:10.1016/j.ejon.2013.08.004 · Cited by 37
“Ancestry informative markers (AIMs) were used to minimize confounding due to population stratification (Halder et al., 2008; Hoggart et al., 2003; Tian et al., 2008).”
MethodKlimentidis, Y. C., Dulin, A., Casazza, K., Willig, A. L., Allison, D. B., & Fernández, J. R. (2011) · Journal of Human Hypertension · doi:10.1038/jhh.2010.130 · Cited by 35
Lupus risk variants in the PXK locus alter B-cell receptor internalization
Vaughn, S. E., Foley, C. L., Lu, X., Patel, Z. H., Zoller, E. E., Magnusen, A. F., Williams, A. H., Ziegler, J. T., Comeau, M. E., Marion, M. C., et al. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2014.00450 · Cited by 33
Mechanick, J. I., Adams, S., Davidson, J. A., Fergus, I. V., Galindo, R. J., McKinney, K. H., Petak, S. M., Sadhu, A., Samson, S. L., Vedanthan, R., et al. (2019) · Endocrine Practice · doi:10.4158/ps-2019-0080 · Cited by 35
“Biological factors can be evaluated using trans-ancestry (or trans-ethnic) genome-wide association studies (GWASs), exome chip association studies, replication studies, and other individual genetic ancestry estimates and informative markers (95-99).”
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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