Development and forensic evaluation of an 8-dye Multi-InDel multiplex panel for highly degraded samples

The analysis of highly degraded DNA samples remains a significant challenge in forensic genetics. Multi-InDel present several advantages-including high polymorphisms, short amplicons, low mutation rates, and the absence of stutter artifacts-making it an ideal genetic marker for genotyping highly degraded samples. Conventional 5-dye systems commonly used for highly degraded samples often accommodate only a limited number of loci because of the requirement for short amplicons and the restricted number of fluorescent channels. This constraint reduces the forensic efficacy of the system, particularly in paternity testing involving highly degraded samples. As a validated technology, 8-dye fluorescence technology enables the inclusion of more loci with short amplicons and shows considerable promise as an effective tool for the forensic analysis of highly degraded samples. This study introduces an 8-dye Multi-InDel panel capable of simultaneously detecting 28 autosomal Multi-InDel loci. All Multi-InDel loci were engineered to yield amplicons not more than 125 bp in length to enhance compatibility with highly degraded samples. Full genotyping profiles were successfully obtained from samples containing as little as 62.5 pg of DNA. Notably, even after 100 min of thermal degradation at 100°C, the 28 Multi-InDel panel retained an allele detection rate of 100%, whereas the commercial STR kit detected only 26.2% of alleles. The system demonstrated excellent forensic efficiency, with a cumulative matching probability (CMP) of 2.3292 × 10^-18 and a cumulative probability of exclusion (CPE) of 0.9999669. The mean cumulative paternity index (CPI) across the 49 parent-offspring trios was 2.18 × 10⁷, and all 2352 Mendelianinconsistent trios were correctly excluded from paternity. Taken together, our results demonstrate that the 28 Multi-InDel panel performed in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, and could be a practical, robust, and efficient strategy for the forensic identification of highly degraded samples.