Autosomal SNP Assays

Participants: Peter M. Vallone, Amy E. Decker, and John M. Butler

Project Timeframe: July 2002 to present

Purpose: To examine the utility of bi-allelic single nucleotide polymorphism (SNP) markers to differentiate between individuals present in major U.S. populations.

Progress: Initially, a total of 189 samples from 3 different U.S. sample groups {Caucasian (74), African American (71), and Hispanic (44)} were typed for 70 autosomal genetic markers.  These 70 markers are bi-allelic (C/T) short nucleotide polymorphisms (SNPs).  For each sample, the 70 SNP markers were typed in 11 unique 6-plexes and a single 4-plex PCR.  Information on the 70 SNPs along with other classes of SNP markers can be found at ..\SNP.htm and ..\SNPs\OrchidSNPinfo.htm. A total of 10 of the 210 tests (70 loci x 3 populations) for Hardy-Weinberg equilibrium indicated a statistically significant result.  In order to evaluate the minimum number of SNP loci needed to distinguish all 189 samples from one another, the loci were ranked according to their levels of observed heterozygosity and p-values obtained on testing for Hardy-Weinberg equilibrium. The top 12 loci according to these ranking criteria were tabulated along with the number of unique genotypes observed when combining subsequent SNP markers. 

The 12 selected SNPs possessed an observed heterozygosity of >0.45 in all three populations examined and thus would be expected to exhibit more differences between samples. All 189 samples in this study were individualized with a subset of 12 SNP loci.  However, it is likely that the addition of more than 12 SNP loci will be required to resolve larger sets of unrelated individuals from one another. By way of comparison, in these same 189 individuals all but one pair are resolved from one another with three of the traditional short tandem repeat (STR) loci possessing the highest heterozygosity values (D2S1338, D18S51, and FGA) run with the Identifiler kit. The final pair of unrelated samples could be resolved with the combination of 4 STR loci: D2S1338, D18S51, FGA, and VWA. A 12-plex autosomal SNP assay has been optimized for typing degraded DNA samples and compared to miniSTRs in terms of sensitivity and potential for typing shed hairs.

Publications or Presentations Resulting From This Project:

Vallone, P.M., Decker, A.E., and Butler, J.M. (2005) Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African American, and Hispanic samples. Forensic Sci. Int. 149: 279-286.

Vallone, P.M., Decker, A.E., Coble, M.D., Butler, J.M. (2006) Evaluation of an autosomal SNP 12-plex assay. Progress in Forensic Genetics 11, Elsevier Science: Amsterdam, The Netherlands, International Congress Series 1288, 61-63.

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Last updated: 06/19/2007

Disclaimer: This project was supported by National Institute of Justice Grant Number 2003-IJ-R-029, which is an interagency agreement between NIJ and the NIST Office of Law Enforcement Standards, 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. Certain commercial equipment, instruments and materials are identified in order to specify experimental procedures as completely as possible.  In no case does such identification imply a recommendation or endorsement by the National Institute of Standards and Technology nor does it imply that any of the materials, instruments or equipment identified are necessarily the best available for the purpose.