Characterization of U.S. population samples using a 34plex ancestry informative SNP multiplex

Abstract

The number, scope, and ease of typing of single nucleotide polymorphism (SNP) markers makes them ideal supplements to existing forensic markers sets. SNP typing panels offer additional benefits such as the ability to type degraded DNA, paternity analysis, and the opportunity to infer externally visible traits. SNP also carry the potential to infer the most likely population of origin of an individual using SNPs with highly differentiated allele frequency distributions. One recent example is a 34-plex assay developed by Phillips et al. using SNaPshot primer extension reactions [1]. A significant amount of population information has already been generated, published, and uploaded to the SPSmart open access SNP browsers [2]. The original work by Phillips et al. analyzing the CEPH population diversity panel indicated a low error rate of ancestry prediction when confining comparisons to the three major population groups of Europe, Africa and East Asia. However, admixed populations commonly found in the U.S. represent a significant source of error or at least reduced assignment probabilities when making ancestry predictions. Thorough and wide population surveys in areas where admixture is the predominant pattern, is an important part of the process of assessing this potential source of classification error. In order to contribute to the data already available to end-users, we have generated allele frequencies for a set of U.S. African Americans, Caucasian and Hispanics for 34 ancestry informative SNPs. The data accumulated should contribute to improved characterization of admixed U.S. populations and their analysis through SNP genotyping.