Human Genetics

, Volume 121, Issue 3–4, pp 305–317 | Cite as

Candidate SNPs for a universal individual identification panel

  • Andrew J. Pakstis
  • William C. Speed
  • Judith R. Kidd
  • Kenneth K. Kidd
Original Investigation

Abstract

Single nucleotide polymorphisms (SNPs) are likely in the near future 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. Here we report on progress in identifying SNPs that show little allele frequency variation among a worldwide sample of 40 populations, i.e., have a low Fst, while remaining highly informative. 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 our previously described strategy for both identifying and characterizing such SNPs (Kidd et al. in Forensic Sci Int 164:20–32, 2006), we 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 our 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.

Keywords

Human identification SNPs Forensics Population genetics Fst Heterozygosity 

Supplementary material

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Andrew J. Pakstis
    • 1
  • William C. Speed
    • 1
  • Judith R. Kidd
    • 1
  • Kenneth K. Kidd
    • 1
  1. 1.Department of GeneticsYale University School of MedicineNew HavenUSA

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