Novel Plexor (TM) SNP genotyping technology: Comparisons with TaqMan (R) and homogenous MassEXTEND (TM) MALDI-TOF mass Spectrometry

Analysis of SNPs for association, linkage, haplotype, and pharmacogenetic studies has led to a dramatic increase in the number and evolution of medium, to high throughput genotyping technologies. This study introduces Plexor(TM) as a new method for medium-throughput (single SNP) genotyping. We compare this fluorescent,based chemistry for call rate, accuracy, affordability, throughput, and overall efficiency against two commonly used technologies. These include fluorescent-based TaqMan((R)) allelic discrimination for single SNP analysis (medium-throughput) and the homogenous MassEXTEND(TM) (hME(TM)) chemistry using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for multiple SNP analysis (high-throughput). Analysis of 11 SNPs, including all six possible nucleotide substitutions, showed Plexor TM to be highly comparable for both call rate (94.7%) and accuracy (99.2%) to the TaqMan((R)) (94.6% and 99.8%, respectively) and hME(TM) (91.9% and 98.1%, respectively) chemistries. We demonstrate that this novel method is an efficient, cost-effective alternative to TaqMan((R)) genotyping commonly used in diagnostic settings.