Human Y-chromosome haplotyping by allele-specific polymerase chain reaction

Tenzin Gayden, Maria Regueiro, Laisel Martinez, Alicia M. Cadenas, Rene J. Herrera

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


We describe the application of allele-specific (AS-PCR) for screening biallelic markers, including SNPs, within the nonrecombining region of the human Y-chromosome (NRY). The AS-PCR method is based on the concept that the perfectly annealed primer-template complex is more stable, and therefore, more efficiently amplified under the appropriate annealing temperature than the complex with a mismatched 3′-residue. Furthermore, a mismatched nucleotide at the primer's 3′-OH end provides for a poor extension substrate for Taq DNA polymerase, allowing for discrimination between the two alleles. This method has the dual advantage of amplification and detection of alleles in a single expeditious and inexpensive procedure. The amplification conditions of over 50 binary markers, mostly SNPs, that define the major Y-haplogroups as well as their derived lineages were optimized and are provided for the first time. In addition, artificial restriction sites were designed for those markers that are not selectively amplified by AS-PCR. Our results are consistent with allele designations derived from other techniques such as RFLP and direct sequencing of PCR products.

Original languageEnglish (US)
Pages (from-to)2419-2423
Number of pages5
Issue number11
StatePublished - Jun 2008
Externally publishedYes


  • Allele-specific primers
  • Biallelic marker
  • Mismatch
  • Single nucleotide polymorphisms

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Clinical Biochemistry


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