Forensic analysis of formalin-fixed non-paraffin-embedded tissues: a comparative study of STR and mtDNA profiling

Formalin fixation is a common practice for preserving forensic samples in developing countries like India, but it can adversely affect DNA quality and hinder downstream molecular analyses. This study investigated the effectiveness of mitochondrial DNA (mtDNA) typing in formalin-fixed, non-paraffin-embedded tissues when conventional Short Tandem Repeat (STR) profiling fails due to DNA degradation. Tissue samples from 30 deceased individuals were fixed in 10% unbuffered formalin and divided into four groups based on fixation duration (1-4 weeks). DNA was extracted, quantified, and subjected to STR profiling. Samples with incomplete STR profiles underwent mtDNA sequencing targeting the hypervariable regions to assess maternal lineage and haplogroup distribution. DNA quantification revealed significant degradation across all groups, with decreasing DNA concentrations over time. STR profiling showed limited success, with only 13 out of 27 loci amplified in group 1 and 7 loci in group 2, while groups 3 and 4 yielded no STR profiles. In contrast, mtDNA typing was successful in all samples, revealing distinct haplogroups and haplotypes. Haplogroup M was the most prevalent (50%), with 12 distinct subhaplogroups identified. The presence of East Asian (A11, G1b) and West Eurasian (H10g, T2H2, HV2a, U, R) haplogroups reflects historical migrations and admixture in the Indian population. The study highlights the limitations of STR profiling in formalin-fixed tissues and demonstrate the robustness of mtDNA typing. Incorporating mtDNA analysis into forensic protocols can enhance the reliability and comprehensiveness of DNA profiling results, particularly when dealing with challenging samples. Further research is needed to refine tissue preservation methods and optimize DNA recovery from formalin-fixed tissues to advance molecular analyses in forensic and retrospective studies.