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Kosoy, R., Nassir, R., Tian, C., White, P. A., Butler, L. M., Silva, G. et al. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum. Mutat. 30, 69-78

Rowe Program in Human Genetics, Department of Biochemistry, University of California Davis, Davis, California 95616, USA.
Human Mutation (Impact Factor: 5.14). 01/2009; 30(1):69-78. DOI: 10.1002/humu.20822
Source: PubMed

ABSTRACT

To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome-wide distribution, and genotype reproducibility on two platforms (TaqMan assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations.

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    • "c o m / l o c a t e / f s i g have shown the suitability of SNP markers for use with degraded samples7891011. Also during this time period, publications in both the forensic and clinical realms have characterized SNPs suitable for human identification [12] and ancestry determination [13,14]. In early 2014, a commercial multiplex SNP assay for human identity (HID) applications became available for the Ion Torrent Personal Genome Machine (Ion PGM) (Thermo Fisher Scientific, Waltham, MA, USA) and the HID-Ion AmpliSeq Identity Community Panel (Thermo Fisher Scientific), which allows simultaneous genotyping of 90 autosomal and 30 Y-SNP markers chosen for forensic identification purposes. "
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    • "We evaluated the genomic ancestries of the patients and controls following the methodology of Kosoy et al. (2009), with an in-house modification consisting of the genotyping of 12 genetic ancestry markers (Coelho et al. 2014, unpublished observations). The cases and controls presented the following similar distributions of genomic contribution: approximately 60% contribution from European , 23% from African and 17% from Amerindian ancestral populations. "
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    Full-text · Article · Nov 2014 · Memórias do Instituto Oswaldo Cruz
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    • "The inclusion of ancestry informative markers could help reduce this threat ( Kosoy et al . , 2009 ) . Future directions that manipulate the dopaminergic system through phar - macology or dietary depletion may provide supporting evidence for these findings ( e . g . , use of a medication with D4 properties such as olanzapine to lend credence to initial association findings ; Hutchison et al . , 2003 ) . Similarly , more comprehensive"
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