Multiplex Assay for Comprehensive Genotyping of Genes Involved in Drug Metabolism, Excretion, and Transport

• Published in: Clinical chemistry (Baltimore, Md.) Vol. 53; no. 7; pp. 1222 - 1230
• Main Authors: Daly, Thomas M, Dumaual, Carmen M, Miao, Xin, Farmen, Mark W, Njau, Reuben K, Fu, Dong-Jing, Bauer, Nancy L, Close, Sandra, Watanabe, Nancy, Bruckner, Carsten, Hardenbol, Paul, Hockett, Richard D
• Format: Journal Article
• Language: English
• Published: Washington, DC Am Assoc Clin Chem 01-07-2007; American Association for Clinical Chemistry; Oxford University Press
• Subjects: Accuracy; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Biological Transport - genetics; Drug therapy; Excretion; Fundamental and applied biological sciences. Psychology; Genes; Genetic diversity; Genetic variance; Genetic Variation; Genotype; Genotype & phenotype; Genotypes; Humans; Investigative techniques, diagnostic techniques (general aspects); Medical sciences; Metabolism; Molecular structure; Mutation; Oligonucleotide Array Sequence Analysis; Oligonucleotide Probes; Patients; Pharmaceutical Preparations - metabolism; Pharmacogenetics - methods; Pharmacokinetics; Plasmids; Polymerase Chain Reaction - methods; Polymorphism, Single Nucleotide; Probes; Reproducibility of Results; Technological change; Drug; Excretion; Gene; Clinical biology; Genotype; Genetics; Biochemistry; Pharmacokinetics; Molecular biology; Metabolism; Transport
• ISSN: 0009-9147; 1530-8561
• DOI: 10.1373/clinchem.2007.086348

Drug metabolism is a multistep process by which the body disposes of xenobiotic agents such as therapeutic drugs. Genetic variation in the enzymes involved in this process can lead to variability in a patient's response to medication.
We used molecular-inversion probe technology to develop a multiplex genotyping assay that can simultaneously test for 1227 genetic variants in 169 genes involved in drug metabolism, excretion, and transport. Within this larger set of variants, we performed analytical validation of a clinically defined core set of 165 variants in 27 genes to assess accuracy, imprecision, and dynamic range.
In a test set of 91 samples, genotyping accuracy for the core set probes was 99.8% for called genotypes, with a 1.2% no-call (NC) rate. The majority of the core set probes (133 of 165) had < or = 1 genotyping failure in the test set; a subset of 12 probes was responsible for the majority of failures (mainly NC). Genotyping results were reproducible upon repeat testing with overall within- and between-run variation of 1.1% and 1.4%, respectively-again, primarily NCs in a subset of probes. The assay showed stable genotyping results over a 6-fold range of input DNA.
This assay generates a comprehensive assessment of a patient's metabolic genotype and is a tool that can provide a more thorough understanding of patient-to-patient variability in pharmacokinetic responses to drugs.