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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
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 [29]
The Survey of World Populations Using Individual BGA Estimates (page unavailable) reports that European Americans more frequently showed East Asian, African, and Indigenous American admixture than continental Europeans. The passages do not establish that this ancestry was poorly quantified or that estimates were discordant even within studies. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Inference of Population Structure Using Multilocus Genotype Data
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000) · Genetics · doi:10.1093/genetics/155.2.945 · Cited by 33,871 · see citing works
GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism
Raymond, M., & Rousset, F. (1995) · Journal of Heredity · doi:10.1093/oxfordjournals.jhered.a111573 · Cited by 16,187 · see citing works
Falush, D., Stephens, M., & Pritchard, J. K. (2003) · Genetics · doi:10.1093/genetics/164.4.1567 · Cited by 7,920 · see citing works
Genetic Structure of Human Populations
Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kídd, K. K., Анатольевич, Ж. Л., & Feldman, M. W. (2002) · Science · doi:10.1126/science.1078311 · Cited by 3,000 · see citing works
Interrogating a high-density SNP map for signatures of natural selection.Preprint
Akey, J., Zhang, G., Zhang, K., Jin, L., & Shriver, M. (2002) · Genome Research · doi:10.1101/gr.631202 · Cited by 932 · see citing works
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 · see citing works
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× · see citing works
“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
Kennedy, G., Matsuzaki, H., Dong, S.-L., Liu, W.-M., Huang, J., Liu, G., Su, X., Cao, M., Chen, W., Zhang, J., et al. (2003) · Nature Biotechnology · doi:10.1038/nbt869 · Cited by 609 · see citing works
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 · see citing works
Self-citationAn E-M algorithm and testing strategy for multiple-locus haplotypes.
Long, J. C., Williams, R. C., & Urbanek, M. (1995) · Europe PMC (PubMed Central) · Cited by 533 · see citing works
Control of confounding of genetic associations in stratified populations
Hoggart, C. J., Parra, E. J., Shriver, M. D., Bonilla, C., Kittles, R. A., Clayton, D. G., & McKeigue, P. M. (2003) · The American Journal of Human Genetics · doi:10.1086/375613 · Cited by 490 · see citing works
Self-citationA High-Density Admixture Map for Disease Gene Discovery in African Americans
Smith, M. W., Patterson, N., Lautenberger, J. A., Truelove, A. L., McDonald, G. J., Waliszewska, A., Kessing, B. D., Malasky, M. J., Scafe, C., Le, E., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/420856 · Cited by 459 · see citing works
Ethnic-affiliation estimation by use of population-specific DNA markers.
Shriver, M. D., Smith, M. W., Li, J., Marcini, A., Akey, J. M., Deka, R., & Ferrell, R. E. (1997) · PubMed · Cited by 382 · see citing works
Self-citationHuman Population Genetic Structure and Inference of Group Membership
Bamshad, M. J., Wooding, S., Watkins, W. S., Ostler, C. T., Batzer, M. A., & Jorde, L. B. (2003) · The American Journal of Human Genetics · doi:10.1086/368061 · Cited by 330 · see citing works
Design and analysis of admixture mapping studies.
Hoggart, C., Shriver, M., Kittles, R., Clayton, D., & McKeigue, P. (2004) · American Journal of Human Genetics · doi:10.1086/420855 · Cited by 320 · see citing works
Self-citationJobling, M. A., Hurles, M. E., & Tyler‐Smith, C. (2019) · Garland Science eBooks · doi:10.1201/9780203487211 · Cited by 318 · see citing works
Zegura, S. L. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msh009 · Cited by 299 · see citing works
The Use of Racial, Ethnic, and Ancestral Categories in Human Genetics Research
* (2005) · The American Journal of Human Genetics · doi:10.1086/491747 · Cited by 287 · see citing works
Pfaff, C., Parra, E., Bonilla, C., Hiester, K., McKeigue, P., Kamboh, M., Hutchinson, R., Ferrell, R., Boerwinkle, E., & Shriver, M. (2001) · American Journal of Human Genetics · doi:10.1086/316935 · Cited by 271 · see citing works
Self-citationY-Chromosome Evidence for Differing Ancient Demographic Histories in the Americas
Bortolini, M. C., Salzano, F. M., Thomas, M., Stuart, S., Nasanen, S. P. K., Bau, C. H. D., Hutz, M. H., Layrisse, Z. E., Petzl‐Erler, M. L., Tsuneto, L. T., et al. (2003) · The American Journal of Human Genetics · doi:10.1086/377588 · Cited by 263 · see citing works
Self-citationThe genomic distribution of population substructure in four populations using 8,525 autosomal SNPs
Shriver, M., Kennedy, G., Parra, E., Lawson, H. A., Sonpar, V. A., Huang, J., Akey, J., & Jones, K. (2004) · Human Genomics · doi:10.1186/1479-7364-1-4-274 · Cited by 253 · see citing works
Self-citationCruciani, F., Fratta, R. L., Santolamazza, P., Sellitto, D., Pascone, R., Moral, P., Watson, E., Guida, V., Béraud-Colomb, É., Zaharova, B., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/386294 · Cited by 238 · see citing works
McKeigue, P., Carpenter, J., Parra, E., & Shriver, M. (2000) · Annals of Human Genetics · doi:10.1046/j.1469-1809.2000.6420171.x · Cited by 230 · see citing works
Self-citationGene admixture in human populations: Models and predictions
Chakraborty, R. (1986) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330290502 · Cited by 218 · see citing works
The dual origin and Siberian affinities of Native American Y chromosomes
Lell, J. T., Sukernik, R. I., Starikovskaya, Y. B., Su, B., Jin, L., Schurr, T. G., Underhill, P. A., & Wallace, D. C. (2002) · The American Journal of Human Genetics · doi:10.1086/338457 · Cited by 209 · see citing works
Exact tests for association between alleles at arbitrary numbers of loci
Zaykin, D. V., Zhivotovsky, L. A., & Weir, B. S. (1995) · Genetica · doi:10.1007/bf01441162 · Cited by 200 · see citing works
Lao, O., van Duijn, K., Kersbergen, P., de Knijff, P., & Kayser, M. (2006) · American Journal of Human Genetics · doi:10.1086/501531 · Cited by 192 · see citing works
Tian, C., Hinds, D., Shigeta, R., Kittles, R., Ballinger, D., & Seldin, M. (2006) · American Journal of Human Genetics · doi:10.1086/507954 · Cited by 178 · see citing works
Hanis, C. L., Chakraborty, R., Ferrell, R. E., & Schull, W. J. (1986) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330700404 · Cited by 177 · see citing works
Bonilla, C., Parra, E. J., Pfaff, C., Dios, S., Marshall, J. A., Hamman, R. F., Ferrell, R. E., Hoggart, C., McKeigue, P., & Shriver, M. (2004) · Annals of Human Genetics · doi:10.1046/j.1529-8817.2003.00084.x · Cited by 164 · see citing works
Self-citationReiner, A. P., Ziv, E., Lind, D. L., Nievergelt, C. M., Schork, N. J., Cummings, S. R., Phong, A., Burchard, E. G., Harris, T. B., Psaty, B. M., et al. (2005) · The American Journal of Human Genetics · doi:10.1086/428654 · Cited by 155 · see citing works
Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation
Shriver, M. D., Mei, R., Parra, E. J., Sonpar, V. A., Halder, I., Tishkoff, S. A., Schurr, T. G., Zhadanov, S. I., Osipova, L. P., Brutsaert, T. D., et al. (2005) · Human Genomics · doi:10.1186/1479-7364-2-2-81 · Cited by 150 · see citing works
Self-citationYang, N., Li, H., Criswell, L. A., Gregersen, P. K., Alarcón-Riquelme, M. E., Kittles, R. A., Shigeta, R., SILVA, G. H. D. O., Patel, P. I., Belmont, J. W., et al. (2005) · Human Genetics · doi:10.1007/s00439-005-0012-1 · Cited by 143 · see citing works
Bonilla, C., Shriver, M., Parra, E., Jones, A., & Fernández, J. R. (2004) · Human Genetics · doi:10.1007/s00439-004-1125-7 · Cited by 137 · see citing works
Self-citationEthnic-difference markers for use in mapping by admixture linkage disequilibrium.
Collins-Schramm, H. E., Phillips, C. M., Operario, D., Lee, J. S., Weber, J., Hanson, R., Knowler, W., Cooper, R., Li, H.-Z., & Seldin, M. (2002) · American Journal of Human Genetics · doi:10.1086/339368 · Cited by 135 · see citing works
POPULATION GENETICS, HISTORY, AND HEALTH PATTERNS IN NATIVE AMERICANS
Mulligan, C. J., Hunley, K., Cole, S., & Long, J. C. (2004) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.5.061903.175920 · Cited by 118 · see citing works
Silva, W. A., Bonatto, S. L., Holanda, A. J., Ribeiro‐dos‐Santos, Â., Paixão, B. M., Goldman, G. H., Abe‐Sandes, K., Rodríguez-Delfín, L., Barbosa, M. D. M., Paçó‐Larson, M. L., et al. (2002) · The American Journal of Human Genetics · doi:10.1086/341358 · Cited by 117 · see citing works
Tsai, H., Choudhry, S., Naqvi, M., Rodríguez-Cintrón, W., Burchard, E. G., & Ziv, E. (2005) · Human Genetics · doi:10.1007/s00439-005-0067-z · Cited by 102 · see citing works
Measuring and using admixture to study the genetics of complex diseases
Halder, I., & Shriver, M. D. (2003) · Human Genomics · doi:10.1186/1479-7364-1-1-52 · Cited by 93 · see citing works
Self-citationAdmixture analysis of a rural population of the state of Guerrero, Mexico
Bonilla, C., Gutiérrez, G., Parra, E. J., Kline, C., & Shriver, M. D. (2005) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20227 · Cited by 88 · see citing works
Self-citationRelation of risk of systemic lupus erythematosus to west African admixture in a Caribbean population
Molokhia, M., Hoggart, C., Patrick, A. L., Shriver, M. D., Parra, E. J., Ye, J., Silman, A. J., & McKeigue, P. (2003) · Human Genetics · doi:10.1007/s00439-002-0883-3 · Cited by 82 · see citing works
Self-citationFrequencies of complex diseases in hybrid populations
Chakraborty, R., & Weiss, K. M. (1986) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330700408 · Cited by 61 · see citing works
Human evolutionary genetics: origins, peoples, and disease (2004)
Rockman, M. V. (2004) · Human Genetics · doi:10.1007/s00439-004-1138-2 · Cited by 57 · see citing works
- Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
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 · see citing works
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 610 · see citing works
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 531 · see citing works
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 368 · see citing works
“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 · see citing works
“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…”
ResultInfluentialForensically Relevant SNP Classes
Budowle, B., & van Daal, A. (2008) · BioTechniques · doi:10.2144/000112806 · Cited by 298 · see citing works
Pereira, R., Phillips, C., Pinto, N., Santos, C., dos Santos, S. E. B., Amorim, A., Carracedo, Á., & Gusmão, L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029684 · Cited by 260 · see citing works
“[43].”
Forensic genetic analysis of bio-geographical ancestry
Phillips, C. (2015) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2015.05.012 · Cited by 257 · see citing works
“Eventually the component SNP details were published in 2008 [40] just before DNAprint ceased”
Modeling 3D Facial Shape from DNA
Claes, P. D., 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 247 · see citing works
“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 · see citing works
“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 219 · see citing works
“…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 · see citing works
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 185 · see citing works
Nassir, R., Kosoy, R., Tian, C., White, P. A., Butler, L., Silva, G., Kittles, R., Alarcón-Riquelme, M., Gregersen, P., Belmont, J., et al. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-39 · Cited by 174 · see citing works
“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 ].”
MethodResultInfluentialIlli, J., Miaskowski, C. A., Cooper, B. A., Levine, J. D., Dunn, L. B., West, C. M., Dodd, M. J., Dhruva, A., Paul, S. M., Baggott, C., et al. (2012) · Cytokine · doi:10.1016/j.cyto.2012.02.015 · Cited by 185 · see citing works
“Ancestry informative markers (AIMs) can be used as a tool to minimize confounding due to population stratification in case-control association studies [82–84].”
MethodKidd, J. R., Friedlaender, F. R., Speed, W. C., PAKSTIS, A. J., Vega, F. M. D. L., & Kídd, K. K. (2011) · Investigative Genetics · doi:10.1186/2041-2223-2-1 · Cited by 184 · see citing works
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 167 · see citing works
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 149 · see citing works
“[19]; 128 of the American population analysis panel of Kosoy et al.”
Sætrom, P., Biesinger, J., Li, S. M., Smith, D., Thomas, L. F., Majzoub, K., Rivas, G. E., Alluin, J., Rossi, J. J., Krontiris, T. G., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-1201 · Cited by 138 · see citing works
“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 · see citing works
“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 · see citing works
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 · see citing works
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 · see citing works
The Ethnic/Racial Variations of Intracerebral Hemorrhage (ERICH) Study Protocol
Woo, D., Rosand, J. M., Kidwell, C. S., McCauley, J. L., Osborne, J., Brown, M. W., West, S. E., Rademacher, E. W., Waddy, S. P., Roberts, J. N., et al. (2013) · Stroke · doi:10.1161/strokeaha.113.002332 · Cited by 117 · see citing works
“21 We will use existing software such as Structure 22 and Admixmap 23, 24 to compute individual admixture proportion.”
MethodPopulation admixture associated with disease prevalence in the Boston Puerto Rican health study
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 112 · see citing works
“[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 · see citing works
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 · see citing works
“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 · see citing works
McCann, B., Miaskowski, C. A., Koetters, T., Baggott, C., West, C. M., Levine, J. D., Elboim, C., Abrams, G., Hamolsky, D., Dunn, L. B., et al. (2012) · Journal of Pain · doi:10.1016/j.jpain.2011.02.358 · Cited by 91 · see citing works
Lao, O., Vallone, P. M., Coble, M. D., Diegoli, T. M., van Oven, M., van der Gaag, K. J., Pijpe, J., de Knijff, P., & Kayser, M. (2010) · Human Mutation · doi:10.1002/humu.21366 · Cited by 91 · see citing works
Daya, M., van der Merwe, L., Galal, U., Möller, M., Salie, M., Chimusa, E. R., Galanter, J., van Helden, P. D., Henn, B. M., Gignoux, C. R., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0082224 · Cited by 88 · see citing works
Lessard, C. J., Adrianto, I., Kelly, J. A., Kaufman, K. M., Grundahl, K. M., Adler, A., Williams, A. H., Gallant, C. J., Anaya, J., Bae, S., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.11.014 · Cited by 84 · see citing works
“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 · see citing works
“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 · see citing works
“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 82 · see citing works
Jin, Y., Schäffer, A. A., Feolo, M., Holmes, J. B., & Kattman, B. L. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200925 · Cited by 81 · see citing works
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 81 · see citing works
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 80 · see citing works
Watherston, J., McNevin, D., Gahan, M., Bruce, D., & Ward, J. (2018) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2018.08.016 · Cited by 63 · see citing works
Multilocus OCA2 genotypes specify human iris colors
Frudakis, T., Terravainen, T., & Thomas, M. J. (2007) · Human Genetics · doi:10.1007/s00439-007-0401-8 · Cited by 67 · see citing works
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 · see citing works
A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia
Li, C., PAKSTIS, A. J., Jiang, L., Wei, Y., Sun, Q.-F., Wu, H., Bülbül, Ö., Wang, P., Kang, L., Kidd, J. R., et al. (2016) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2016.04.002 · Cited by 72 · see citing works
“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 · see citing works
“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 70 · see citing works
“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 · see citing works
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 69 · see citing works
“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 70 · see citing works
“…(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 · see citing works
Manta, F. S. D. N., Pereira, R., Caiafa, A., Da, S., Gusmão, L., & de Carvalho, E. F. (2012) · Annals of Human Biology · doi:10.3109/03014460.2012.742138 · Cited by 67 · see citing works
“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 · see citing works
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 66 · see citing works
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 · see citing works
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 · see citing works
Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans
Kersbergen, P., van Duijn, K., Kloosterman, A., den Dunnen, J. D., Kayser, M., & de Knijff, P. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-69 · Cited by 71 · see citing works
“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 58 · see citing works
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 · see citing works
“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 · see citing works
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 · see citing works
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 · see citing works
“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 · see citing works
“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 · see citing works
“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 · see citing works
“…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 · see citing works
“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 55 · see citing works
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 · see citing works
“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 · see citing works
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 · see citing works
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 51 · see citing works
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 · see citing works
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 · see citing works
“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 · see citing works
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 · see citing works
“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 · see citing works
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 · see citing works
“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 43 · see citing works
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 · see citing works
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 42 · see citing works
“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 · see citing works
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 · see citing works
“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 · see citing works
“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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 39 · see citing works
Lee, S., Epstein, M. P., Duncan, R., & Lin, X. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21621 · Cited by 39 · see citing works
“…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 · see citing works
“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., Pai, A., Walker, A., Zeigler-Johnson, C., Gueye, S., Schurr, T., & Rebbeck, T. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007842 · Cited by 38 · see citing works
“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 · see citing works
“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 36 · see citing works
“[37] refer to 170 AIMs; however, their supplementary data file refers to 176 AIMs.”
BackgroundCleveland, H., Schlomer, G., Vandenbergh, D., Feinberg, M., Greenberg, M., Spoth, R., Redmond, C., Shriver, M., Zaidi, A. A., & Hair, K. L. (2015) · Development and Psychopathology · doi:10.1017/s0954579414001291 · Cited by 40 · see citing works
Self-citationSingle Nucleotide Polymorphisms and Applications
Butler, J. M. (2011) · Elsevier eBooks · doi:10.1016/b978-0-12-374513-2.00012-9 · Cited by 37 · see citing works
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 · see citing works
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 · see citing works
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 36 · see citing works
“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 34 · see citing works
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 · see citing works
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 34 · see citing works
“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
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
