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

• NCJ Number: 206529
• Journal: Journal of Forensic Sciences Volume: 49 Issue: 4 Dated: July 2004 Pages: 723-732
• Date Published: July 2004
• Length: 10 pages
• Grant Number(s): 99-IJ-R-094
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical)

Annotation

In order to assess the usefulness of Y-chromosome SNP (single nucleotide polymorphism) markers for human identity applications, this experiment constructed several novel multiplex ASPE (allele-specific primer extension) assays and used a new commercial ASH (allele-specific hybridization) kit to type 50 Y-SNP markers in more than 200 individuals; by examining 10 of the Y-SNP's with both methods, the study assessed concordance in more than 2,000 allele calls between primer extension and hybridization approaches.

Abstract

The study used extracted DNA for 20 U.S. Caucasian and 20 African-American samples. All samples were examined with 15 autosomal short tandem repeats and the amelogenin sex-typing markers. A total of 229 male samples were typed (115 African-Americans and 114 Caucasians). A total of 50 Y-chromosome biallelic markers were used to cover all 18 major haplogroups (A-R) recognized by the Y-chromosome consortium. Y-SNP typing was accomplished with ASH, using the commercially available SignetTM Y-SNP Identification System. The overall strategy for multiplex primer design was used as reported by Schoske et al. This paper also describes the procedures for PCR amplification and ASPE assay using fluorescence detection. For certain loci, the allele-specific hybridization method exhibited sizable background signal from the absent alternate allele; however, 100-percent concordance was observed in 10 markers that were typed by the use of both methods. A total of 18 unique haplogroups out of a possible 45 were observed in the African-American and Caucasian males, with the majority of samples being assigned to 2 of the 18 haplogroups. 4 tables, 4 figures, and 31 references