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.
Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA. petev@nist.gov
Peter M
PM
Vallone
John M
JM
Butler
D000483:Alleles; D044383:Black People / Q000235:genetics*; D041322:Chromosomes, Human, Y; D016172:DNA Fingerprinting / Q000379:methods*; D017931:DNA Primers; D005260:Female; D005819:Genetic Markers; D006239:Haplotypes; D006801:Humans; D006824:Hybridization, Genetic; D008297:Male; D020641:Polymorphism, Single Nucleotide; D020080:Tandem Repeat Sequences; D014481:United States; D044465:White People / Q000235:genetics*; D001741:Black or African American
D017931:DNA Primers; D005819:Genetic Markers