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Human Y‐chromosome haplotyping by allele‐specific polymerase chain reaction
Author(s) -
Gayden Tenzin,
Regueiro Maria,
Martinez Laisel,
Cadenas Alicia M.,
Herrera Rene J.
Publication year - 2008
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.200700702
Subject(s) - biology , genetics , primer extension , polymerase chain reaction , primer (cosmetics) , single nucleotide polymorphism , allele , haplotype , microbiology and biotechnology , in silico pcr , dna , gene , multiplex polymerase chain reaction , genotype , chemistry , base sequence , organic chemistry
We describe the application of allele‐specific PCR (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.