Biological samples, including
skeletal remains exposed to environmental insults for extended periods of time, exhibit increasing levels of DNA damage and fragmentation. Human forensic identification methods typically use a combination of mitochondrial (mt)
DNA sequencing and short tandem repeat (STR) analysis, which target segments of
DNA ranging from 80 to 500 base pairs (bps). Larger templates are often unavailable as skeletal samples age and the associated
DNA degrades. Single-nucleotide polymorphism (SNP) loci target shorter templates and may serve as a
solution to the problem. Recently developed assays for STR and SNP analysis using a massively parallel sequencing approach, such as the ForenSeq kit (Verogen, San Diego, CA), offer a means for generating results from degraded samples as they target templates down to 60 to 170 bps. We performed a modeling study that demonstrates that SNPs can increase the significance of an identification when analyzing
DNA down to an average size of 100 bps for input amounts between 0.375 and 1 ng of nuclear
DNA. Observations from this study were then compared with human skeletal material results (n = 14, ninth to eighteenth centuries), which further demonstrated the utility of the ForenSeq kit for degraded samples. The robustness of the
Promega PowerSeq™ Mito System was also tested with human
skeletal remains (n = 70, ninth to eighteenth centuries), resulting in successful coverage of 99.29% of the
mtDNA control region at 50× coverage or more. This was accompanied by modifications to a mainstream
DNA extraction technique for
skeletal remains that improved recovery of shorter templates.