Novel Y-STRs with elevated mutation rates further improve male relative differentiation

Y-chromosomal short tandem repeats (Y-STRs) with elevated mutation rates are valuable markers for distinguishing male suspects from their paternal male relatives - something that is typically not possible with standard Y-STRs. However, while the 26 rapidly mutating Y-STRs (RM Y-STRs) we identified in our two previous screens substantially improve male relative differentiation compared to standard Y-STRs, many close relatives cannot be separated with these markers. Aiming to further enhance the discrimination power of male relatives, particularly closely related ones, we performed a new chromosome-wide search for Y-STRs with elevated mutation rates by integrating in-silico marker discovery with experimental marker verification. Relative to previous screens, three major advancements were applied: (1) use of the Y-chromosome sequence from the telomere-to-telomere reference genome and other genomes, (2) consideration of all repeat motifs from homopolymers to hexanucleotides, and (3) use of targeted massively parallel sequencing to genotype male relatives for marker verification. To ensure robust allele calling and mutation detection for dinucleotide repeats prone to PCR slippage, we developed and applied a novel curve-fitting approach that accounts for all observed signals: true alleles and stutter products. Overall, we identified 14 novel Y-STRs with previously unreported elevated mutation rates, most of which were dinucleotide repeats. Relative to the 30-marker set of the RMplex tool, this novel set increased the empirical differentiation rates of close relatives separated by 1-4 meioses by 20.0%, 15.6%, 9.9% and 4.1%, respectively. The combined set of 44 novel and previous markers empirically differentiated 46.9%, 80.4%, 86.4%, and 84.8% of close relatives separated by 1-4 meioses and 96.4-100% of distant relatives separated by 5-15 meioses. The differentiation capacities of this 44-marker set, estimated from locus-specific mutation rates, were 50.2%, 75.2%, 87.6%, and 93.8% for these close relatives and 96.9-100% for the distant ones. Provided the development and successful forensic validation of a targeted genotyping tool, we anticipate that this expanded set of 44 Y-STRs with elevated mutation rates will enhance the ability to distinguish a male suspect from his paternal male relatives. This will benefit solving criminal cases where an autosomal STR profile of the male perpetrator cannot be generated and where standard Y-STR profiling yields a haplotype match between the suspect and the trace as well as haplotype sharing between the suspect and his male relative(s).