title: Characterization of 107 genomic DNA reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1: a GeT-RM and Association for Molecular Pathology collaborative project.
abstract: Pharmacogenetic testing is becoming more common; however, very few quality control and other reference materials that cover alleles commonly included in such assays are currently available. To address these needs, the Centers for Disease Control and Prevention's Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing community and the Coriell Cell Repositories, have characterized a panel of 107 genomic DNA reference materials for five loci (CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1) that are commonly included in pharmacogenetic testing panels and proficiency testing surveys. Genomic DNA from publicly available cell lines was sent to volunteer laboratories for genotyping. Each sample was tested in three to six laboratories using a variety of commercially available or laboratory-developed platforms. The results were consistent among laboratories, with differences in allele assignments largely related to the manufacturer's assay design and variable nomenclature, especially for CYP2D6. The alleles included in the assay platforms varied, but most were identified in the set of 107 DNA samples. Nine additional pharmacogenetic loci (CYP4F2, EPHX1, ABCB1, HLAB, KIF6, CYP3A4, CYP3A5, TPMT, and DPD) were also tested. These samples are publicly available from Coriell and will be useful for quality assurance, proficiency testing, test development, and research.
authors.affiliation: Quest Diagnostics Nichols Institute, Chantilly, Virginia, USA.
authors.forename: Victoria M
authors.initials: VM
authors.lastname: Pratt
authors.forename: Barbara
authors.initials: B
authors.lastname: Zehnbauer
authors.forename: Jean Amos
authors.initials: JA
authors.lastname: Wilson
authors.forename: Ruth
authors.initials: R
authors.lastname: Baak
authors.forename: Nikolina
authors.initials: N
authors.lastname: Babic
authors.forename: Maria
authors.initials: M
authors.lastname: Bettinotti
authors.forename: Arlene
authors.initials: A
authors.lastname: Buller
authors.forename: Ken
authors.initials: K
authors.lastname: Butz
authors.forename: Matthew
authors.initials: M
authors.lastname: Campbell
authors.forename: Chris
authors.initials: C
authors.lastname: Civalier
authors.forename: Abdalla
authors.initials: A
authors.lastname: El-Badry
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Farkas
authors.forename: Elaine
authors.initials: E
authors.lastname: Lyon
authors.forename: Saptarshi
authors.initials: S
authors.lastname: Mandal
authors.forename: Jason
authors.initials: J
authors.lastname: McKinney
authors.forename: Kasinathan
authors.initials: K
authors.lastname: Muralidharan
authors.forename: LeAnne
authors.initials: L
authors.lastname: Noll
authors.forename: Tara
authors.initials: T
authors.lastname: Sander
authors.forename: Junaid
authors.initials: J
authors.lastname: Shabbeer
authors.forename: Chingying
authors.initials: C
authors.lastname: Smith
authors.forename: Milhan
authors.initials: M
authors.lastname: Telatar
authors.forename: Lorraine
authors.initials: L
authors.lastname: Toji
authors.forename: Anand
authors.initials: A
authors.lastname: Vairavan
authors.forename: Carlos
authors.initials: C
authors.lastname: Vance
authors.forename: Karen E
authors.initials: KE
authors.lastname: Weck
authors.forename: Alan H B
authors.initials: AH
authors.lastname: Wu
authors.forename: Kiang-Teck J
authors.initials: KT
authors.lastname: Yeo
authors.forename: Markus
authors.initials: M
authors.lastname: Zeller
authors.forename: Lisa
authors.initials: L
authors.lastname: Kalman
mesh_terms: D000483:Alleles; D001189:Aryl Hydrocarbon Hydroxylases / Q000235:genetics*; D002460:Cell Line; D065731:Cytochrome P-450 CYP2C19; D065729:Cytochrome P-450 CYP2C9; D019389:Cytochrome P-450 CYP2D6 / Q000235:genetics*; D004247:DNA / Q000235:genetics; D005819:Genetic Markers; D015894:Genome, Human; D005838:Genotype; D014453:Glucuronosyltransferase / Q000235:genetics*; D006801:Humans; D006899:Mixed Function Oxygenases / Q000235:genetics*; D057089:Pathology, Molecular / Q000295:instrumentation / Q000379:methods; D010597:Pharmacogenetics / Q000295:instrumentation / Q000379:methods; D064417:Vitamin K Epoxide Reductases; D000099148:UGT1A1 Enzyme
chemical_list: D001189:Aryl Hydrocarbon Hydroxylases; D065731:Cytochrome P-450 CYP2C19; D065729:Cytochrome P-450 CYP2C9; D019389:Cytochrome P-450 CYP2D6; D004247:DNA; D005819:Genetic Markers; D014453:Glucuronosyltransferase; D006899:Mixed Function Oxygenases; D064417:Vitamin K Epoxide Reductases; D000099148:UGT1A1 Enzyme; C450260:CYP2C9 protein, human; C045793:CYP2C19 protein, human; C578523:VKORC1 protein, human