A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications
- PMID: 18286470
- DOI: 10.1002/humu.20695
A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications
Abstract
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.
Similar articles
-
Ancestry informative markers in Amerindians from Brazilian Amazon.Am J Hum Biol. 2008 Jan-Feb;20(1):86-90. doi: 10.1002/ajhb.20681. Am J Hum Biol. 2008. PMID: 17963227
-
Informativeness of the CODIS STR loci for admixture analysis.J Forensic Sci. 2005 Nov;50(6):1322-6. J Forensic Sci. 2005. PMID: 16382826
-
Development of two multiplex mini-sequencing panels of ancestry informative SNPs for studies in Latin Americans: an application to populations of the State of Minas Gerais (Brazil).Genet Mol Res. 2010 Oct 19;9(4):2069-85. doi: 10.4238/vol9-4gmr911. Genet Mol Res. 2010. PMID: 20967697
-
Using ancestry-informative markers to define populations and detect population stratification.J Psychopharmacol. 2006 Jul;20(4 Suppl):19-26. doi: 10.1177/1359786806066041. J Psychopharmacol. 2006. PMID: 16785266 Review.
-
Admixture and clinical phenotypic variation.Hum Hered. 2014;77(1-4):73-86. doi: 10.1159/000362233. Epub 2014 Jul 29. Hum Hered. 2014. PMID: 25060271 Review.
Cited by
-
Levels of Genital Tract Defensins and Cytokines Differ between HIV-Uninfected US and African Women.Am J Reprod Immunol. 2015 Oct;74(4):313-22. doi: 10.1111/aji.12411. Epub 2015 Jun 21. Am J Reprod Immunol. 2015. PMID: 26094732 Free PMC article. Clinical Trial.
-
African Genetic Ancestry is Associated with Sleep Depth in Older African Americans.Sleep. 2015 Aug 1;38(8):1185-93. doi: 10.5665/sleep.4888. Sleep. 2015. PMID: 25845688 Free PMC article.
-
Circadian rhythm phase shifts and endogenous free-running circadian period differ between African-Americans and European-Americans.Sci Rep. 2015 Feb 11;5:8381. doi: 10.1038/srep08381. Sci Rep. 2015. PMID: 25670162 Free PMC article.
-
Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?BMC Med Genomics. 2018 Nov 20;11(Suppl 5):0. doi: 10.1186/s12920-018-0412-4. BMC Med Genomics. 2018. PMID: 30453954 Free PMC article.
-
Looking for race in all the wrong places: analyzing the lack of productivity in the ongoing debate about race and genetics.Hum Genet. 2009 Sep;126(3):355-62. doi: 10.1007/s00439-009-0674-1. Epub 2009 Apr 25. Hum Genet. 2009. PMID: 19396464 Review.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical
Miscellaneous