title: A novel simple method for determining CYP2D6 gene copy number and identifying allele(s) with duplication/multiplication.
abstract: BACKGROUND
  Cytochrome P450 2D6 (CYP2D6) gene duplication and multiplication can result in ultrarapid drug metabolism and therapeutic failure or excessive response in patients. Long range polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequencing are usually used for genotyping CYP2D6 duplication/multiplications and identification, but are labor intensive, time consuming, and costly.
  
  
  METHODS
  We developed a simple allele quantification-based Pyrosequencing genotyping method that facilitates CYP2D6 copy number variation (CNV) genotyping while also identifying allele-specific CYP2D6 CNV in heterozygous samples. Most routine assays do not identify the allele containing a CNV. A total of 237 clinical and Coriell DNA samples with different known CYP2D6 gene copy numbers were genotyped for CYP2D6 *2, *3, *4, *6, *10, *17, *41 polymorphisms and CNV determination.
  
  
  RESULTS
  The CYP2D6 gene allele quantification/identification were determined simultaneously with CYP2D6*2, *3, *4, *6, *10, *17, *41 genotyping. We determined the exact CYP2D6 gene copy number, identified which allele had the duplication or multiplication, and assigned the correct phenotype and activity score for all samples.
  
  
  CONCLUSIONS
  Our method can efficiently identify the duplicated CYP2D6 allele in heterozygous samples, determine its copy number in a fraction of time compared to conventional methods and prevent incorrect ultrarapid phenotype calls. It also greatly reduces the cost, effort and time associated with CYP2D6 CNV genotyping.
authors.affiliation: Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Taimour
authors.initials: T
authors.lastname: Langaee
authors.affiliation: Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Issam
authors.initials: I
authors.lastname: Hamadeh
authors.affiliation: Renal Division, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Arlene B
authors.initials: AB
authors.lastname: Chapman
authors.affiliation: Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, United States of America.
authors.forename: John G
authors.initials: JG
authors.lastname: Gums
authors.affiliation: Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Julie A
authors.initials: JA
authors.lastname: Johnson
mesh_terms: D000483:Alleles; D019389:Cytochrome P-450 CYP2D6 / Q000235:genetics*; D056915:DNA Copy Number Variations; D018628:Gene Dosage; D020440:Gene Duplication; D005787:Gene Frequency; D060005:Genotyping Techniques; D006801:Humans; D010641:Phenotype; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D019389:Cytochrome P-450 CYP2D6