Performance of microarray genotyping and massively parallel sequencing for dense SNP profiling of challenged skeletal remains

Dense single nucleotide polymorphism (SNP) profiling is central to forensic genetic genealogy (FGG), but challenged forensic samples frequently contain degraded DNA, low quantities of human DNA, and substantial microbial contamination. Although microarrays perform well with high-quality DNA, their performance with challenged forensic specimens is limited. Microarray performance was evaluated on a dilution series of high-quality control DNA and on DNA extracts from 10 skeletal remains that previously yielded successful SNP profiles with massively parallel sequencing (MPS). The skeletal samples represented a range of degradation index values, human DNA quantities, and proportions of human DNA. The high-quality sample series demonstrated robust microarray performance. However, most challenged skeletal samples generated microarray profiles with markedly reduced or inflated heterozygosity, poor signal-to-noise ratios, and large numbers of discordant genotype calls compared with MPS data despite call rates that would traditionally be considered acceptable. Thus, call rate alone can overestimate microarray profile quality with challenged forensic samples; successful microarray genotyping depends on more than human DNA quantity. Because forensic evidence is often limited and irreplaceable, analytical approaches that maximize the likelihood of successful SNP recovery should be prioritized. These findings support MPS as the preferred platform for dense SNP profiling of challenged forensic specimens.