Genetic Chaos

Monday, April 26, 2004

Multiplexed assays for evaluation of Y-SNP markers in US populations

Genetic markers located on the Y chromosome are of increasing importance in human identity testing. In an effort to evaluate the forensic utility of Y chromosome single nucleotide polymorphism (SNP) markers, we constructed several novel multiplex allele-specific primer extension (ASPE) assays and utilized a new commercial allele-specific hybridization (ASH) multiplex kit to examine 50 Y-SNP markers in 229 males from two US Caucasian and African American populations. The novel ASPE assays covered 18 Y-SNP markers in three multiplex reactions while a commercial ASH kit was used to type 42 Y-SNPs plus amelogenin for sex-typing purposes. There were 10 overlapping loci between the ASPE and ASH methods permitting an evaluation of concordance on over 2000 allele calls. The 50 Y-SNP markers examined in this study define 45 of the 159 possible Y Chromosome Consortium (YCC) haplogroups. Only 18 different haplogroups were observed in our samples.

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

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 are primer extension with fluorescence detection, and allele-specific hybridization using flow cytometry. In this paper, we examined 50 different SNPs on the Y- chromosome using three primer extension multiplexes and five hybridization multiplex assays. For certain loci, the allele-specific hybridization method exhibited sizable background signal from the absent alternate allele. However, 100% concordance (>2000 alleles) was observed in ten 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.

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