PGM and S5: across platform comparison of identity and ancestry informative SNP genotypes

In cases where only apartial or incomplete STR profile is obtained from an evidence sample,information contained in single nucleotide polymorphisms (SNPs) can proveinformative for human identification or investigative leads.... [ view full abstract ]

In cases where only apartial or incomplete STR profile is obtained from an evidence sample,information contained in single nucleotide polymorphisms (SNPs) can proveinformative for human identification or investigative leads. There are a numberof advantages of using SNPs in forensics including that genotypes can beobtained from very small PCR products (generally <100 bp), and they canprovide valuable information in ‘no-hit’ CODIS cases, as they can be selectedto provide insight on bio-geographic ancestry, kinship and externally visiblecharacteristics. ThermoFisher Scientific have released two commercial multiplexSNP panels, that can be typed on either the PGM^™ or the automated S5platform: (1) Precision ID Identity Panel, targeting 124 SNPs that provide uniquegenotypes to distinguish individuals within a single population; and (2)Precision ID Ancestry Panel, targeting 165 SNPs that can discriminate betweenglobal populations to predict the ancestry of a sample. In this study, weprepared libraries in triplicate using 1.0 ng of DNA as input for fivecommercially available pure DNAs (K562, HeLa, Raji, 9948 and 9947A), along withblood extracted from both a male and female donor for both the Precision ID Identityand Ancestry Panel (total n, 42). To allow direct comparison of the performanceof the panels on both the PGM^™ and S5, the resulting libraries weresequenced on both platforms. This poster will outline: 1) a comparison of theperformance metrics (i.e., amplicon strand balance, amplicon heterozygositybalance and amplicon coverage) for each panel on both platforms, 2) anyinstances of genotype discordance among replicates or across platforms, and 3) thenumber of SNPs flagged by the HID SNP Genotyper quality control filter (forcoverage, major allele frequency, strand balance and genotype quality) acrossboth platforms for a given sample. The results presented will provide insightinto the advantages and any potential pitfalls (e.g. lossof data quality and coverage depth) when genotyping either panel on the PGM^™and automated S5 platform.