This article reports on progress in identifying single nucleotide polymorphisms (SNPs) that show little allele frequency variation among a worldwide sample of 40 populations, i.e., have a low Fst, while remaining highly informative.
Soon SNPs are likely to have a fundamental role both in human identification and description; however, because allele frequencies can vary greatly among populations, a critical issue is the population genetics underlying calculation of the probabilities of unrelated individuals having identical multi-locus genotypes. Such markers have match probabilities that are nearly uniform irrespective of population and become candidates for a universally applicable individual identification panel applicable in forensics and paternity testing. They are also immediately useful for efficient sample identification/tagging in large biomedical, association, and epidemiologic studies. Using the authors’ previously described strategy for both identifying and characterizing such SNPs (Kidd et al. in Forensic Sci Int 164:20–32, 2006), they have now screened a total of 432 SNPs likely a priori to have high heterozygosity and low allele frequency variation and from these have selected the markers with the lowest Fst in a set of 40 populations to produce a panel of 40 low Fst, high heterozygosity SNPs. Collectively, these SNPs give average match probabilities of less than 10−16 in most of the 40 populations and less than 10−14 in all but one small, isolated population; the range is 2.02 × 10−17 to 1.29 × 10−13. These 40 SNPs constitute excellent candidates for the global forensic community to consider for a universally applicable SNP panel for human identification. The relative ease with which these markers could be identified also provides a cautionary lesson for investigations of possible balancing selection. 32 references (publisher abstract modified)