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Eurasiaplex: A Forensic SNP Assay for Differentiating European and South Asian Ancestries

NCJ Number
Forensic Science International: Genetics Volume: 7 Issue: 3 Dated: May 2013 Pages: 359-366
C. Phillips; A. Freire Aradas; A. K. Kriegel; M. Fondevila; O. Bulbul; C. Santos; F. Serrulla Rech,; M. D. Perez Carceles; Á. Carracedo; P. M. Schneider; M. V. Lareu
Date Published
May 2013
8 pages
Researchers have selected a set of single nucleotide polymorphisms (SNPs) with the specific aim of differentiating European and South Asian ancestries.
The SNPs were combined into a 23-plex SNaPshot primer extension assay: Eurasiaplex, designed to complement an existing 34-plex forensic ancestry test with both marker sets occupying well-spaced genomic positions, enabling their combination as single profile submissions to the Bayesian Snipper forensic ancestry inference system. The researchers analyzed the ability of Eurasiaplex plus 34plex SNPs to assign ancestry to a total 1648 profiles from 16 European, 7 Middle East, 13 Central-South Asian and 21 East Asian populations. Ancestry assignment likelihoods were estimated from Snipper using training sets of five-group data (three Eurasian groups, East Asian and African genotypes) and four-group data (Middle East genotypes removed). Five-group differentiations gave assignment success of 91 percent for NW European populations, 72 percent for Middle East populations and 39 percent for Central-South Asian populations, indicating Middle East individuals are not reliably differentiated from either Europeans or Central-South Asians. Four-group differentiations provided markedly improved assignment success rates of 97 percent for most continental Europeans tested (excluding Turkish and Adygei at the far eastern edge of Europe) and 95 percent for Central-South Asians, despite applying a probability threshold for the highest likelihood ratio above '100 times more likely'. As part of the assessment of the sensitivity of Eurasiaplex to analyze challenging forensic material we detail Eurasiaplex and 34-plex SNP typing to infer ancestry of a cranium recovered from the sea, achieving 82 percent SNP genotype completeness. Therefore, Eurasiaplex provides an informative and forensically robust approach to the differentiation of European and South Asian ancestries amongst Eurasian populations. (Published Abstract)