Screening of microhaplotypes for paternity testing from low-recombination regions in the human genome

Microhaplotypes are playing an increasingly important role in forensic evidence analysis. However, the impact of meiotic recombination events on the efficacy of microhaplotypes in paternity testing remains poorly understood. Based on the data from the 1000 Genomes Project and a high-resolution recombination map, we identified microhaplotypes from low recombination-rate regions (recombination rate < 0.1 cM/Mb) and validated their efficacy for paternity testing by assessing their performance in 580 trio families and in simulated datasets. The results showed that: (1) The low-recombination microhaplotypes outperformed their high-recombination counterparts in paternity testing; (2) A panel of 30 microhaplotypes, selected from low-recombination, non-coding regions of the autosomes, achieved a cumulative power of discrimination (CPD) of 1-6.77 × 10− 37 and cumulative probability of exclusion (CPE) of 1-1.72 × 10− 13; (3) Validation using real-world trios demonstrated that low-recombination microhaplotypes had significantly higher cumulative paternity index (CPI) values (p < 2e-16), outperforming conventional STR markers by seven orders of magnitude; (4) Simulation analyses revealed that low-recombination markers could distinguish true parentage with 100% accuracy and had higher paternity testing accuracy compared to high-recombination counterparts; (5) An online microhaplotype database (http://bioinformatics.gqliulab.com/microhaplotype/) was established, enabling users to query information and calculate forensic parameters. An open-access microhaplotype screening tool, MHpatools, was developed and is freely available at http://bioinformatics.gqliulab.com/MHpatools/. Collectively, the established microhaplotype system, database, and analytical tools would be useful in forensic genetics.