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Multiplexed Assays for Evaluation of Y-SNP Markers in U.S. Populations



Peter Vallone, John Butler


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 U.S. Caucasian and African American populations. The novel ASPE assays covered 18 Y-SNP markers in 3 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 2,000 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.
Proceedings Title
International Congress Series; Progress in Forensic Genetics 10
Conference Dates
September 9-13, 2003
Conference Location
Arcachon, FR
Conference Title
20th International Congress of the International-Society-for-Forensic-Genetics


allele-specific hybridization, forensic science, primer extension, single nucleotide polymorphism, SNP typing, Y chromosome, Y-SNPs


Vallone, P. and Butler, J. (2004), Multiplexed Assays for Evaluation of Y-SNP Markers in U.S. Populations, International Congress Series; Progress in Forensic Genetics 10, Arcachon, FR (Accessed April 12, 2024)
Created March 31, 2004, Updated October 15, 2021