Monday, August 27, 2012

Development of a Customized PGx Genotyping Array using key variants in PharmGKB

The University of Florida and Stanford University are undertaking a joint pharmacogenetics implementation project funded by the NIH, piloted first at Florida and replicated at Stanford. Initially, CYP2C19 genotype will be used to guide clopidogrel therapy, however a customized array of SNPs from 120 genes involved in drug response was designed for preemptive genotyping. This enables a patient's genotype information to be available in the future if or when a drug is to be prescribed. Read more in the Clinical Pharmacology & Therapeutics article available online.

Selecting SNPs for the array included one or more the following:

1. There is a PharmGKB Clinical Annotation written between the SNP and a drug response, usually with high levels of evidence.
2. It is a functional SNP within a VIP
3. It is a known tag SNPs for an important PGx haplotype
4. It is a SNP of interest to the research groups

to give:
252 PGx SNPs (listed in the Supplementary Information) + 2 sex markers + 2 SNPs for quality control

Details of the genotyping array technology, validation, costs and turnaround times are outlined. Also discussed in the article are the current potential barriers to clinical implementation of pharmacogenetics, and how a preemptive genotyping approach can overcome some of these.

J A Johnson, B M Burkley, T Y Langaee, M J Clare-Salzler, T E Klein and R B Altman. Clinical Pharmacology & Therapeutics (2012); advance online publication 22 August 2012. doi:10.1038/clpt.2012.125