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Rapid SNP Genotyping of the Pharmacogenomically Important Allele CYP2D6*4 Using Real-Time qPCR on the DNA Engine Opticon 2 System

lor real-time protocol on the DNA Engine Opticon 2 system. The protocol uses two hydrolysis probes labeled with two different fluorophores, FAM and VIC, to distinguish between the wild-type G nucleotide and the variant A nucleotide at position 1934 of the CYP2D6 gene. After completion of the assay, each sample was automatically assigned to one of three groups, homozygous GG, homozygous AA, or heterozygous GA, by an analysis feature of the Opticon Monitor software.

This assay is a valuable tool for pharmacogenomics, in which genotype information can be used to design the most effective drug therapy for an individual patient. The short time (total of 3 hours) required for the qPCR run and data analysis, and the ability to perform reactions in a 96-well format should allow this assay to be used for routine genotyping in a clinical setting. In our patient population, the nine patients who carried two copies of the variant allele were classified as poor metabolizers. For these patients, a poorly metabolized drug could be avoided, or the dose and course of drug administration could be reduced, to avoid any adverse effects that might occur with a standard course of drug therapy. The ability of the Opticon 2 system to unequivocally distinguish between the three SNP genotypes in both the control and the patient DNA samples, and the availability of TaqMan assays for SNP analysis of other alleles in the CYP2D6 gene and other genes, demonstrate that the Opticon 2 system is an effective platform for a wide range of SNP genotype assays.6


References
1. McElroy, S., Sachse, C., Brockmoller, J., Richmond, J., Lira, M., Friedman, D., Roots, I., Silber, B. M. and Milos, P. M. CYP2D6 geno
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