Human Y-chromosome SNP characterization by multiplex amplified product-length polymorphism analysis

Area of Science:

• Genetics
• Anthropology
• Molecular Biology

Background:

• Y-chromosome Single Nucleotide Polymorphism (SNP) typing is crucial for defining paternal lineage phylogeny.
• Existing methods like SNaPshot™ and PCR-RFLP are costly and require specialized equipment.
• Low-quality DNA often presents challenges for accurate SNP typing.

Purpose of the Study:

• To design an optimized allele-specific amplification protocol for Y-chromosome SNP typing.
• To provide a cost-effective and efficient alternative to current SNP typing technologies.
• To enable accurate phylogenetic analysis using minimal and low-quality DNA samples.

Main Methods:

• Developed an allele-specific amplification protocol using Amplification Fragment Length Polymorphism (AFLP).
• Utilized primers with noncomplementary nucleotide tails to differentiate SNP alleles by fragment size.
• Designed a single reaction to simultaneously define up to six mutations.

Main Results:

• The protocol achieved highly specific definition of multiple Y-chromosome SNPs in a single reaction.
• Successfully typed major Y clades (E, F, K, R, Q) and numerous subhaplogroups.
• Demonstrated compatibility with as little as 0.5 ng of DNA, including low-quality samples.
• Generated amplification fragments ranging from 60 to 158 bp for clade and subhaplogroup identification.

Conclusions:

• The developed allele-specific amplification protocol is a cost-effective and efficient method for Y-chromosome SNP typing.
• This technique is suitable for defining phylogenetic status of paternal lineages, even with limited or degraded DNA.
• Offers a valuable tool for population genetics, anthropology, and forensic applications.