Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension

J Forensic Sci. 2004 Jul;49(4):723-32.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alleles
  • Black People / genetics*
  • Chromosomes, Human, Y*
  • DNA Fingerprinting / methods*
  • DNA Primers
  • Female
  • Genetic Markers
  • Haplotypes
  • Humans
  • Hybridization, Genetic
  • Male
  • Polymorphism, Single Nucleotide
  • Tandem Repeat Sequences*
  • United States
  • White People / genetics*


  • DNA Primers
  • Genetic Markers