Title: Developmental validation of Y-SNP pedigree tagging system: A panel via quick ARMS PCR

Area of Science:

• Genetics
• Forensic Science
• Population Genetics

Background:

• Y chromosomal short tandem repeats (Y-STRs) are widely used for paternal relatedness and population substructure analysis.
• Y-STR applications are limited in resolving close relationships and differentiating individuals from diverse geographic origins.

Purpose of the Study:

• To introduce a novel Y-SNP multiplex typing strategy using rapid ARMS PCR.
• To develop a Y-SNP Pedigree Tagging System for efficient and accurate Y-SNP profiling.

Main Methods:

• Developed a multiplex PCR assay to profile 24 Y-SNPs and 13 sub-haplogroups in a single reaction.
• Validated the system for degraded DNA, sensitivity, specificity, reproducibility, stability, and performance in various scenarios, including mixture studies and population surveys.
• Applied the system to analyze father-son/brother-brother pairs and two Chinese Han populations.

Main Results:

• The Y-SNP Pedigree Tagging System profiles 24 Y-SNPs and 13 sub-haplogroups in 4-5 hours.
• Consistent Y-SNP patterns were observed in 40 father-son or brother-brother pairs.
• Distinct distribution patterns of male donors were identified in two Chinese Han populations, aiding in pedigree discrimination.

Conclusions:

• The Y-SNP Pedigree Tagging System is a robust and reliable tool for male haplogroup determination.
• This system overcomes Y-STR limitations, offering enhanced resolution for paternal lineage and population substructure studies.
• The system is valuable for determining haplogroup affiliation and resolving East Asian population substructures.