Novel Plexor™ SNP genotyping technology: comparisons with TaqMan ® and homogenous MassEXTEND™ 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™ 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 ® allelic discrimination for single SNP analysis (medium‐throughput) and the homogenous MassEXTEND™ (hME™) 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™ to be highly comparable for both call rate (94.7%) and accuracy (99.2%) to the TaqMan ® (94.6% and 99.8%, respectively) and hME™ (91.9% and 98.1%, respectively) chemistries. We demonstrate that this novel method is an efficient, cost‐effective alternative to TaqMan ® genotyping commonly used in diagnostic settings. Hum Mutat 28(9), 922–927, 2007. © 2007 Wiley‐Liss, Inc.