title: Multiplex assay for comprehensive genotyping of genes involved in drug metabolism, excretion, and transport.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Daly
authors.forename: Carmen M
authors.initials: CM
authors.lastname: Dumaual
authors.forename: Xin
authors.initials: X
authors.lastname: Miao
authors.forename: Mark W
authors.initials: MW
authors.lastname: Farmen
authors.forename: Reuben K
authors.initials: RK
authors.lastname: Njau
authors.forename: Dong-Jing
authors.initials: DJ
authors.lastname: Fu
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Bauer
authors.forename: Sandra
authors.initials: S
authors.lastname: Close
authors.forename: Nancy
authors.initials: N
authors.lastname: Watanabe
authors.forename: Carsten
authors.initials: C
authors.lastname: Bruckner
authors.forename: Paul
authors.initials: P
authors.lastname: Hardenbol
authors.forename: Richard D
authors.initials: RD
authors.lastname: Hockett
mesh_terms: D001692:Biological Transport / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D004364:Pharmaceutical Preparations / Q000378:metabolism*; D010597:Pharmacogenetics / Q000379:methods*; D010957:Plasmids; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D015345:Oligonucleotide Probes; D004364:Pharmaceutical Preparations