Empirical evaluation of 56 microhaplotypes with cryptic variation for kinship testing in a Korean population

Microhaplotypes (microhaps), composed of two or more SNPs within short DNA segments, have emerged as promising markers for forensic kinship testing, offering advantages over conventional STRs. However, their resolution for distant relationships remains limited, prompting efforts to improve panel performance. This study evaluated a 56-locus microhap panel in a Korean population and examined the effects of incorporating cryptic variations adjacent to established microhap loci, identified through massively parallel sequencing. Using data from 281 individuals across 53 families, the panel demonstrated superior discrimination in parent-child, full-siblings, and second-degree relatives pairs compared with STRs, while resolution for third-degree relatives remained challenging. A total of 72 cryptic variations were detected across 38 loci, increasing the mean effective allele number (A e ) from 3.288 to 3.476 and generating 23 novel haplotypes. Incorporating these variants led to modest but consistent improvements in likelihood ratio distributions across all kinship categories. These findings highlight that leveraging cryptic variations can enhance microhap-based kinship inference without panel redesign, providing a cost-effective and scalable strategy for improving forensic kinship analysis. Further studies in larger and multi-ethnic populations will be essential to validate and optimize this approach for broader forensic applications. • Kinship informativeness of 56 microhap markers was evaluated using empirical data from a Korean population. • Incorporating cryptic variations into the 56-locus microhap panel improved kinship resolution without requiring a redesign of the existing panel. • The study highlights the potential of cryptic variation to enhance microhap-based forensic applications.