Forensic identity SNPs: Characterisation of flanking region variation using massively parallel sequencing

Single nucleotide polymorphisms (SNPs) can be analysed for identity or kinship applications in forensic genetics to either provide an adjunct to traditional STR typing or as a stand-alone approach. The advent of massively parallel sequencing technology (MPS) has provided a useful opportunity to more easily deploy SNP typing in a forensic context, given the ability to simultaneously amplify a large number of markers. Furthermore, MPS also provides valuable sequence data for the targeted regions, which enables the detection of any additional variation seen in the flanking regions of amplicons. In this study we genotyped 977 samples across five UK-relevant population groups (White British, East Asian, South Asian, North-East African and West African) for 94 identity-informative SNP markers using the ForenSeq DNA Signature Prep Kit. Examination of flanking region variation allowed for the identification of 158 additional alleles across all populations studied. Here we present allele frequencies for all 94 identity-informative SNPs, both including and excluding the flanking region sequence of these markers. We also present information on the configuration of these SNPs in the ForenSeq DNA Signature Prep Kit, including performance metrics for the markers and investigation of bioinformatic and chemistry-based discordances. Overall, the inclusion of flanking region variation in the analysing workflow for these markers reduced the average combined match probability 2175 times across all populations, with a maximum reduction of 675,000-fold in the West African population. The gain due to flanking region-based discrimination increased the heterozygosity of some loci above that of some of the least useful forensic STR loci; thus demonstrating the benefit of enhanced analysis of currently targeted SNP markers for forensic applications.

Is MPS always the answer? Use of two PCR-based methods for Y-chromosomal haplotyping in highly and moderately degraded bone material

Forensic and population genetics often rely on Y-chromosomal studies. Whether it is a human identification case, trace evidence examination or phylogenetic analysis, a Y-STR haplotype is an important tool in the hands of law enforcement agencies. A common obstacle in achieving satisfactory results in all of the above mentioned circumstances, is low DNA quantity and quality within samples obtained. In this study we have examined Y-STR haplotypes in 75 bone material samples, coming from different time periods. For this purpose we have chosen YFiler Plus PCR Amplification Kit (ThermoFisher Scientific) and ForenSeq Signature DNA Prep Kit (Verogen Inc.), which use two different allele calling technologies - capillary electrophoresis and Massively Parallel Sequencing respectively. Full profiles were obtained from DNA extracts with as little as 0.1896 ng (Degradation Index 1.3) (ForenSeq) and 0.0591 ng (Degradation Index 26.8) (YFiler Plus) DNA input. The results that we present in this paper show differences in amplification rates between common markers in both kits. The differences strictly reflect mean amplicon length of markers. This, however, does not seem to influence Y-haplogroup estimation results noticeably. In one sample a discordance occurred between haplotypes obtained with both methods, where a 24 allele was called in DYS390 marker by capillary electrophoresis, while for the same sample in this locus a 23 allele was shown with MPS. A reason for this is yet to be investigated. The sequence analysis revealed a significant variation between isometric alleles, especially within repetitive regions of studied Y-STR markers.