Human autosomal SNP profiling using fully automated electrospray ionization time of flight mass spectrometry

Single nucleotide polymorphisms (SNPs) represent a simple yet powerful tool for individual identification. Efforts by Pakstis and Kidd et al. to produce an ideal panel of genetically unlinked binary SNPs with high heterozygosity, low population bias, and uniform distribution over global populations have resulted in a 40-SNP panel analyzed across 40 global populations and a more-recent highly unlinked 45-SNP panel analyzed across 44 global populations. A fully automated PCR/Electrospray ionization mass spectrometry (ESI-MS) assay that genotypes the first 40-marker SNP panel has been developed for the Ibis PLEX-ID™ platform and developmentally validated. A 64-SNP assay that incorporates the union of the two SNP panels has been developed for the Ibis PLEX-ID™ and is undergoing validation. Concordance with standard TaqMan assays for a panel of samples has been demonstrated for all loci. The assay has been characterized for sensitivity, reproducibility, species specificity, and the ability to detect when genotyping results indicate a pure sample or a mixture/contaminated sample. Validation studies suggest sensitivity close to 100. pg DNA per reaction. A convenient software interface has been developed for visual review of automated data analyses. The Ibis PLEX-ID™ ESI-MS platform is capable of running Y-STR, autosomal STR, mitochondrial DNA, and SNP analyses on a single instrument within the same automated run.