Comprehensive Assessment of Metabolic Enzyme and Transporter Genes Using the Affymetrix ^® Targeted Genotyping System

Abstract

The combined effects of multiple polymorphisms in several drug-metabolizing enzyme and transporter genes can contribute to considerable interindividual variation in drug disposition and response. Therefore, it has been of increasing interest to generate scalable, flexible and cost-effective technologies for large-scale genotyping of the drug-metabolizing enzyme and transporter genes. However, the number of drug-metabolizing enzyme and transporter gene variants exceeds the capacity of current technologies to comprehensively assess multiple polymorphisms in a single, multiplexed assay. The Targeted Genotyping System (Affymetrix, CA, USA) provides a solution to this challenge, by combining molecular inversion probe technology with universal microarrays to provide a method that is capable of analyzing thousands of variants in a single reaction, while remaining relatively insensitive to cross-reactivity between reaction components. This review will focus on the Targeted Genotyping System and how this technology was adapted to enable comprehensive analysis of drug-metabolizing enzyme and transporter gene polymorphisms.

Cytochrome P450 Genetic Polymorphisms and the Response to Prasugrel

“…Genotyping was performed with the use of the Affymetrix Targeted Human DMET (drug-metabolizing enzymes and transporters) 1.0 Assay (Affymetrix, Santa Clara, Calif; 98% of genotypes) 28 and bidirectional sequencing or exon-specific polymerase chain reaction amplification followed by restriction fragment length polymorphism gel electrophoresis in the case of CYP2C19*17 or a no-call on the DMET chip (2% of genotypes). A total of 54 alleles, comprising the known major functional variants, were determined with the use of clinically validated assays for CYP2C19, CYP2C9, CYP2B6, CYP3A5, CYP3A4, and CYP1A2 (Table III in the online-only Data Supplement).…”

CYP4F2 genetic variant alters required warfarin dose

“…23 The laboratory protocol followed the standard process described in the Targeted Genotyping System User Guide, 24 except for a preliminary PCR amplification step aimed at resolving genotypes from 29 SNPs in 14 regions containing pseudogenes and close homologs. 25 The region containing CYP4F2 was not included in this class of preamplified genes.…”

Prediction of In Vivo Clearance and Associated Variability of CYP2C19 Substrates by Genotypes in Populations Utilizing a Pharmacogenetics-Based Mechanistic Model

“…The CYP2C19 genotyping was conducted using the Drug Metabolizing Enzyme and Transporter Gene assay system (v.1 and v.2; Affymetrix, Santa Clara, CA) (Dumaual et al, 2007) in good laboratory practicecompliant laboratories (Eli Lilly and Company, Indianapolis, IN). Additionally, CYP2C19*17 (rs12248560, 2806C.T) was supplementally tested by either TaqMan (assay ID: C_469857_10; Applied Biosystems, Foster City, CA) at Eli Lilly and Company or Sanger sequencing at Polymorphic DNA Technologies (Alameda, CA).…”