title: SNP genotyping using TaqMan technology: the CYP2D6*17 assay conundrum.
abstract: CYP2D6 contributes to the metabolism of many clinically used drugs and is increasingly tested to individualize drug therapy. The CYP2D6 gene is challenging to genotype due to the highly complex nature of its gene locus. TaqMan technology is widely used in the clinical and research settings for genotype analysis due to assay reliability, low cost, and the availability of commercially available assays. The assay identifying 1023C>T (rs28371706) defining a reduced function (CYP2D6*17) and several nonfunctional alleles, produced a small number of unexpected diplotype calls in three independent sets of samples, i.e. calls suggested the presence of a CYP2D6*4 subvariant containing 1023C>T. Gene resequencing did not reveal any unknown SNPs in the primer or probe binding sites in any of the samples, but all affected samples featured a trio of SNPs on their CYP2D6*4 allele between one of the PCR primer and probe binding sites. While the phenomenon was ultimately overcome by an alternate assay utilizing a PCR primer excluding the SNP trio, the mechanism causing this phenomenon remains elusive. This rare and unexpected event underscores the importance of assay validation in samples representing a variety of genotypes, but also vigilance of assay performance in highly polymorphic genes such as CYP2D6.
authors: 1] Division of Clinical Pharmacology, Toxicology &Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO [2] Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO.
authors: Andrea
authors: A
authors: Gaedigk
authors: Tanenbaum Centre for Pharmacogenetics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
authors: Natalie
authors: N
authors: Freeman
authors: Thermo Fisher Scientific, Genetic Analysis, South San Francisco, CA.
authors: Toinette
authors: T
authors: Hartshorne
authors: Division of Clinical Pharmacology, Toxicology &Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO.
authors: Amanda K
authors: AK
authors: Riffel
authors: Tanenbaum Centre for Pharmacogenetics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
authors: David
authors: D
authors: Irwin
authors: Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN.
authors: Jeffrey R
authors: JR
authors: Bishop
authors: Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA.
authors: Mark A
authors: MA
authors: Stein
authors: Department of Psychiatry, Mount Sinai School of Medicine, New York, NY.
authors: Jeffrey H
authors: JH
authors: Newcorn
authors: The University of The West Indies, Department of Paraclinical Sciences, St. Augustine, Trinidad and Tobago.
authors: Lazara Karelia Montané
authors: LK
authors: Jaime
authors: Department of Psychiatry, University of California San Diego, La Jolla, CA.
authors: Mariana
authors: M
authors: Cherner
authors: 1] Division of Clinical Pharmacology, Toxicology &Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO [2] Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO.
authors: J Steven
authors: JS
authors: Leeder
mesh_terms: D000483:Alleles; D001483:Base Sequence; D001665:Binding Sites; D019389:Cytochrome P-450 CYP2D6 / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics / Q000378:metabolism; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D019389:Cytochrome P-450 CYP2D6