Y-SNP Typing of U.S. African American and Caucasian Samples Using Allele-Specific Hybridization and Primer Extension

ABSTRACT: Multiplex analysis of genetic markers has become increasingly important in a number of fields including DNA diagnostics and human identity testing. Two methods for examination of single nucleotide polymorphisms (SNPs) with a potential for a high degree of multiplex analysis of markers include primer extension with fluorescence detection and allele-specific hybridization using flow cytometry. In this work, we examined 50 different SNPs on the Y-chromosome using 3 primer extension multiplexes and 5 hybridization multiplex assays. For certain loci, the allele-specific hybridization method exhibited sizable background signal from the absent alternate
allele. However, 100% concordance (>2,000 alleles) was observed in 10 markers that were typed using both methods. A total of 18 unique haplogroups out of a possible 45 were observed in a group of 229 U.S. African American and Caucasian males with the majority of samples being assigned into 2 of the 18 haplogroups.