Biomarkers in the era of personalized medicine - a multiplexed SNP assay using capillary electrophoresis for assessing drug metabolism capacity

Abstract

Pharmacogenetics is the study of genetic differences in an individual that leads to variability in drug response. Single-nucleotide polymorphisms (SNPs) prove to be important determinants in evaluating and predicting a patient's response to certain medications and risk of adverse events. The Cytochrome P450 2D6 (CYP2D6) gene is particularly important in the metabolism of many clinically prescribed drugs. In this study, we designed a multiplexed panel to interrogate 8 clinically relevant SNPs of CYP2D6 (*2 at C2856G, *2 at G4181C, *3, *4, *5,*6, *7, and *8). We PCR-amplified a 4.7 kB segment of the CYP2D6 locus containing all the SNPs of interest using genomic DNA extracted from whole blood. Using single base extension and capillary electrophoresis separation, peaks corresponding to the SNPs resolve within a 25-60 bp window. We subsequently analyzed 25 samples using this protocol and compared results to traditional DNA sequencing using an ABI 3730. All samples were 100% concordant between the two methods. This assay can be performed with <24 h turnaround time and minimal hands-on effort. This multiplex SNP panel can be used for interrogation of 8 SNPs within the 2D6 gene, with application to identifying poor metabolizers of 2d6. Patients harbouring SNPs in 2D6 could be triaged to alternative therapies in an effort to maximize therapeutic efficacy and reduce adverse drug reactions.