A nanopore sequencing scheme for MiniHap markers and its application in kinship analysis

Kinship testing based on genetic correlation is one of the primary tasks in forensic genetics. Currently, microhaplotypes (MHs) have become a research hotspot in the field of forensic genetics. Traditional MHs are defined as tightly linked SNPs within short fragments of up to 300 bp. In recent years, nanopore sequencing technology has advanced rapidly. Leveraging its prominent capability for sequencing long contiguous DNA fragments, it enables the detection of longer haplotype markers. MiniHaps are defined as DNA fragments up to 800 bp in length, containing at least five SNPs. Compared to traditional MHs, MiniHaps exhibit significantly higher allele diversity, with a mean effective number of alleles (A_e) exceeding 12. In this proof-of-concept study, we utilized Oxford Nanopore sequencing to investigate haplotype data for 68 selected MiniHaps in 32 individuals from a large real pedigree encompassing kinship relationships up to the ninth degree. Subsequently, allele (haplotype) frequencies, forensic parameters, and the effective number of alleles were calculated. The cumulative match probability (CMP) and cumulative power of exclusion (CPE) for this MiniHap panel were 3.2079 × 10^-132 and 1-1.50636 × 10^-63, respectively. Different analysis methods were applied to both simulated and real data, under assumptions accounting for and ignoring relatedness. The results indicate that the 68 MiniHaps show promise for distinguishing third-degree relative pairs from unrelated individuals. However, their effectiveness for more distant relationships is suboptimal. These findings demonstrate the feasibility of Oxford Nanopore sequencing devices for MiniHap detection and suggest the potential of this novel marker system in kinship analysis.