Chart showing Autosomal SNP 12-plex. NEED BETTER
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 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.  A total of 10 of the 210 tests (70 loci x 3 populations) for Hardy-Weinberg equilibrium indicated a statistically significant result. To evaluate the minimum number of SNP loci needed to distinguish all 189 samples from each other, 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.
 
Information on the 70 SNPs along with other classes of SNP markers can be found at
 
Currently the lab is working on optimizing a 12-plex autosomal SNP assay for typing degraded DNA samples. The performance of the assays will be compared to miniSTRs in terms of sensitivity and potential for typing shed hairs.
  
Publications 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.


This is a National Institute of Justice funded project conducted by the National Institute of Standards and Technology Human Identity Team. This project is supported by Grant Numbers 1999-IJ-R-A094 and 2003-IJ-R-029, which is an interagency agreement between NIJ and the NIST Office of Law Enforcement Standards, awarded by NIJ, Office of Justice Programs, U.S. 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 U.S. 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 NIST nor does it imply that any of the materials, instruments, or equipment identified are necessarily the best available for the purpose.