Differentiating European and South Asian individuals using SNPs and pyrosequencing technology

The population-specific SNP set developed by the SNPforID consortium comprises 34 SNPs enabling accurate differentiation between three major population groups: European, African and East Asian. If a South Asian population (from the Indian subcontinent) was also analyzed, the assignment error rate increased due to a lack of sufficient differentiation between Europeans and South Asians. It was thus necessary to find some alternative SNPs to distinguish these populations. An assay has been designed using pyrosequencing technology for eight candidate SNPs selected from the literature. Using this small SNP panel, a set of samples has been typed from both European and South Asian populations. The frequency data obtained was submitted to a web portal (http://mathgene.usc.es/snipper/) allowing a differentiation algorithm to be produced. A number of samples were then run through this algorithm resulting in a 100% success rate of population identification. (C) 2008 Elsevier Ireland Ltd. All rights reserved.