Initial Evaluation of A96-Plex Goldengate® Genotyping SNP Assay with Suboptimal and Whole Genome Amplified Samples

A custom designed 96-plex GoldenGate® Genotyping single nucleotide polymorphism (SNP) assay was evaluated for performance with genomic samples (10-250ng template), whole genomic amplified (WGA) samples and environmentally challenged samples. The assay performed well with pristine genomic samples, reproducibly generating complete and accurate SNP profiles with lower (50ng) than the manufacturer’s recommended amount of template (250ng). Clinical and forensic samples often fall below the optimal concentration for direct SNP analysis. One proposed solution to this is to produce sufficient quantities of DNA prior to SNP typing by whole genome amplification (WGA). The results of this study show that WGA prior to SNP typing produced reliable results when the template was of high quality and quantity (?10ng). However, SNP-typing of environmentally challenged skeletal samples produced poor results, both with and without WGA prior to SNP typing. The amplification bias inherent in the WGA process was significantly exaggerated with samples of low quality and quantity. While these results suggest that SNP-typing using the Illumina GoldenGate® assay is not the solution for genotyping highly degraded samples, it can provide an alternative means for some forensic DNA typing needs, such as paternity testing or typing reference samples for databasing.