Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs

Area of Science:

• Forensic Genetics
• Population Genetics
• Human Genetics

Background:

• Y-chromosomal short tandem repeats (Y-STRs) are crucial for male lineage tracing and forensic identification.
• Understanding Y-STR mutation rates and variations in specific populations is essential for accurate forensic applications.
• Previous studies have established Y-STR mutation patterns, but population-specific data and advanced typing methods are continuously needed.

Purpose of the Study:

• To genotype 41 Y-STRs in a large cohort of Northern Han Chinese father-son pairs.
• To determine Y-STR haplotype diversity, discrimination capacity, and mutation rates in this population.
• To compare results from massively parallel sequencing (MPS) and capillary electrophoresis (CE) and identify novel genetic variants.

Main Methods:

• Genotyping of 2,548 father-son pairs using 41 Y-STR loci.
• Comparison of MPS and CE typing methods for allele identification, including length-based and variant alleles.
• Sanger sequencing and MPS for mutation confirmation and identification of single nucleotide polymorphisms (SNPs) and deletions.
• Development of the StatsY software for automated calculation of forensic parameters.

Main Results:

• High haplotype diversity (0.999956608) and discrimination capacity (0.96741007) were observed.
• A total of 2,387 unique haplotypes were detected.
• 268 father-son pairs showed mutations at a single locus, with an average Y-STR mutation rate of approximately 3.4 x 10^-3.
• 16 novel repeat region (RR) variant alleles, two SNPs, and one 4-bp deletion were identified.
• The StatsY software was developed for efficient forensic data analysis.

Conclusions:

• The study provides valuable Y-STR data for the Northern Han Chinese population, enhancing forensic identification capabilities.
• Factors such as longer STR regions, complex motifs, and paternal inheritance influence Y-STR mutation rates.
• The development of StatsY offers a significant advancement for automated forensic analysis of Y-STR data.