title: 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.
authors.affiliation: Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA. peter.vallone@nist.gov
authors.forename: Peter M
authors.initials: PM
authors.lastname: Vallone
authors.forename: Amy E
authors.initials: AE
authors.lastname: Decker
authors.forename: John M
authors.initials: JM
authors.lastname: Butler
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods; D005787:Gene Frequency; D005819:Genetic Markers; D005828:Genetics, Population; D006579:Heterozygote; D006801:Humans; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D044469:Racial Groups / Q000235:genetics*; D020080:Tandem Repeat Sequences; D014481:United States
chemical_list: D005819:Genetic Markers