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. KiddEmail author
Original Investigation


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.


Human identification SNPs Forensics Population genetics Fst Heterozygosity 



This work was funded primarily by NIJ Grant 2004-DN-BX-K025 to KKK awarded by the National Institute of Justice, Office of Justice Programs, US Department of Justice. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the US Department of Justice. We thank Applied Biosystems for making their allele frequency database available to us. We also want to acknowledge and thank the following people who helped assemble the samples from the diverse populations: F. L. Black, B. Bonne-Tamir, L. L. Cavalli-Sforza, K. Dumars, J. Friedlaender, L. Giuffra, E. L. Grigorenko, S. L. B. Kajuna, N. J. Karoma, K. Kendler, J-J. Kim, W. Knowler, S. Kungulilo, R-B. Lu, A. Odunsi, F. Okonofua, F. Oronsaye, J. Parnas, L. Peltonen, L. O. Schulz, D. Upson, K. Weiss, and O. V. Zhukova. In addition, some of the cell lines were obtained from the National Laboratory for the Genetics of Israeli Populations at Tel Aviv University, Israel, and the African American samples were obtained from the Coriell Institute for Medical Research, Camden, NJ. Special thanks are due to the many hundreds of individuals who volunteered to give blood samples for studies of gene frequency variation.

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
    Email author
  1. 1.Department of GeneticsYale University School of MedicineNew HavenUSA

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