Simulated Pharmacogenomics Exercises for the Cybertory Virtual Molecular Biology Laboratory

The emerging discipline of pharmacogenomics applies genomic technologies to predict individuals' responses to therapeutic drugs based on the genetic sequences of drug targets and enzymes involved in drug metabolism. The first diagnostic test for genotyping two important drug metabolizing enzymes (CYP450 2D6 and 2C19) has been FDA approved. This assay involves PCR amplification and identification of functionally relevant SNPs using a DNA microarray. We have developed a simulation of PCR and microarray analysis of these important enzymes using the open-source Cybertory(TM) Virtual Molecular Biology Laboratory (www.cybertory.org). Genomic sequences are instantiated from these succinct genotype descriptions by substituting allele sequences onto a framework of the full human reference genome. PCR products can be used as probes for microarray hybridization. Using the Cybertory (TM) microarray image generator[1], we have designed a virtual "SNP chip" to distinguish alleles of CYP450 2D6 based on signal intensities from perfect match and mismatched probe sets.