A High-throughput Real-time PCR Approach to Pharmacogenomics Studies

Toinette Hartshorne

doi:10.4172/2153-0645.1000133

Abstract

Advances in personalized medicine have led to an increase in pharmacogenomics studies that involve testing individuals for drug metabolism enzyme and transporter gene polymorphisms implicated in drug response. As a consequence, there is a growing demand for affordable, easy to use technologies with fast sample-to-results workflows that can accommodate testing customizable sets of target gene variants and a changeable number of samples. Additionally, data analysis tools are needed to facilitate translation of an individual’s genetic information to their diploid content of gene-level star allele haplotypes, which can be correlated with drug metabolism enzyme phenotypes. Here we describe the development of a comprehensive pharmacogenomics experiments workflow solution to meet this need. High quality data was generated from purified buccal swab DNAs run with TaqMan® SNP genotyping and copy number assays in OpenArray® and 384-well plate formats, respectively, on the QuantStudio™ 12K Flex system. Data analysis was accomplished using TaqMan® Genotyper™ Software to examine SNP genotyping assay results and CopyCaller® Software to examine copy number assay results, followed by translation of this genetic data for individual samples to star allele genotypes using the recently developed AlleleTyper™ Software. The specific TaqMan® SNP Genotyping and Copy Number Assays to gene variants used can be tailored to suit the needs of a given pharmacogenomics study. This low cost, high throughput pharmacogenomics workflow can be completed in a single day, from sample preparation to data analysis.

Highlights

Pharmacogenomics (PGx) is the study of genetic variation as it relates to drug response
We demonstrate a high success rate of genotyping calls for drug metabolism enzyme (DME) gene variants through our newly developed workflow, starting with DNA preparation from buccal swabs, proceeding through genotyping using the QuantstudioTM12k Flex Real-time PCR System with TaqMan® single nucleotide polymorphisms (SNPs) Genotyping Assays on OpenArray® Plates and TaqMan® Copy Number Assays on 384-well plates, and concluding with data analysis
Polyester buccal swabs were used for sample collection from 30 unrelated individuals, and DNAs purified from these samples were subjected to both DME gene variant SNP genotyping and copy number variation experiments

Summary

A High-throughput Real-time PCR Approach to Pharmacogenomics Studies

Toinette Hartshorne1*, Ferrier Le1, Jordan Lang, Harrison Leong, Kathleen Hayashibara, Dominique Dewolf and Elliot Shelton1 1Thermo Fisher Scientific, Genomic Applications, South San Francisco, CA, USA 2Thermo Fisher Scientific, Life Sciences Solution, Saint Aubin, France. Received date: April 09, 2014, Accepted date: May 20, 2014, Published date: May 28, 2014

Introduction

Materials and Methods

Results and Discussion