Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples

Abstract

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. In order to evaluate the minimum number of SNP loci needed to distinguish all 189 samples from one another, we ranked the loci according to their levels of observed heterozygosity and p-values obtained upon 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 of the 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 is 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.

STRs vs. SNPs: thoughts on the future of forensic DNA testing

“…While automation of SNP detection has improved significantly in recent years enabling millions of SNPs to be examined on hundreds of samples in a relatively short period of time (e.g., 7), due to the large number of loci that must be co-amplified and the inability to easily decipher mixtures, we do not feel that SNPs stand on the horizon as future markers (i.e., replacing STRs) for widespread use in forensic DNA testing. That being said, there are and will likely be important [20]) are shown in (A). Note that only SNP locus 2 in the top panel of (A) has an allele imbalance suggesting that a possible second contributor is present.…”

Developing a SNP panel for forensic identification of individuals

“…Vallone et al [20] tested 70 SNPs on three populations and found that 12 of them were sufficient to yield a unique genotype for each individual. While our panel of 19 markers did not result in unique genotypes for every individual, we tested over 10 times as many individuals ($2100 versus 189).…”

“…Other SNP panels have been proposed [20][21][22]. While the SNPs have usually been selected for high heterozygosity in the target population, they have not generally been tested in multiple populations.…”

Haplotype block: a new type of forensic DNA markers

“…Therefore, larger SNP panels would be needed for Electronic supplementary material The online version of this article (doi:10.1007/s00414-009-0400-5) contains supplementary material, which is available to authorized users. forensic identification if the same level of discrimination is desired [7][8][9][10][11][12].…”