A novel pharmacogenetic testing panel for CYP2C19 genetic polymorphisms

Specific drug metabolism rates are defined by the constituency of the cytochrome P450 (CYP) genome, including polymorphic changes in any of 200+ CYP genes. An example is CYP2C19, where associations of gene polymorphisms with variability in certain drug metabolism rates have been linked to inter-individual and inter-ethnic differences in therapeutic outcomes. While pharmacogenomic screening for these variants prior to drug and dosage prescription has well-defined links to better treatment outcomes, current implementation is limited to complex and costly variant-probing and DNA sequencing protocols, which have limited availability in clinical laboratories, leading to slow turnaround times, impacting effective clinical intervention. Here we describe a novel, cost-effective, multiplex genotyping approach to screening CYP2C19 variants. Fluorescence nested allele-specific (FAS) PCR was used with primers to detect CYP2C19 variants of interest in specific hot spots, including the Tier 1 haplotypes identified by the Association for Molecular Pathology (AMP): CYP2C19*2, *3, and *17. The presence/absence of wild-type and mutant alleles were identified independently as haplotypes, and in a multiplex reaction as diplotypes representing the 10 possible genotype combinations/profiles. FAS-PCR achieved the same genotype calls as a pyrosequencing protocol optimized for validating genotypes, but with a simpler and more sensitive interface. The FAS-PCR method correctly identified the genotypes of both synthesized DNA and a human genomic DNA standard. Uniquely, the FAS-PCR protocol generates patterns using one fluorescently-labeled primer irrespective of the number of variants targeted, establishing it as considerably more cost-effective than other allele-specific PCR-based techniques that involve labeling both the forward and reverse primers.