Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles A GeT-RM Collaborative Project.

Pharmacogenetic (PGx) testing is increasingly available from clinical and research laboratories. However, only a limited number of quality control and other reference materials (RMs) are currently available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, Centers for Disease Control and Prevention based Genetic Testing Reference Material Coordination Program (GeT-RM), in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories, has characterized 179 DNA samples derived from Coriell cell lines. Testing included the re-characterization of 137 genomic DNAs that were genotyped in previous GeT-RM studies and 42 additional samples that had not been previously characterized. DNA samples were distributed to volunteer testing laboratories for genotyping using a variety of commercially available and laboratory developed tests. These publicly available samples will support the quality assurance and quality control programs of clinical laboratories performing CYP2D6 testing.

[1]  I Zineh,et al.  Cytochrome P4502D6 (CYP2D6) Gene Locus Heterogeneity: Characterization of Gene Duplication Events , 2007, Clinical pharmacology and therapeutics.

[2]  Association for Molecular Pathology statement. Recommendations for in-house development and operation of molecular diagnostic tests. , 1999, American journal of clinical pathology.

[3]  Neil A. Miller,et al.  The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database , 2017, Clinical pharmacology and therapeutics.

[4]  Michelle Whirl-Carrillo,et al.  Standardizing terms for clinical pharmacogenetic test results: consensus terms from the Clinical Pharmacogenetics Implementation Consortium (CPIC) , 2016, Genetics in Medicine.

[5]  A. Gaedigk,et al.  CYP2D6 Haplotype Determination Using Long Range Allele-Specific Amplification: Resolution of a Complex Genotype and a Discordant Genotype Involving the CYP2D6*59 Allele. , 2015, The Journal of molecular diagnostics : JMD.

[6]  Teri E Klein,et al.  Preemptive clinical pharmacogenetics implementation: current programs in five US medical centers. , 2015, Annual review of pharmacology and toxicology.

[7]  Erick R. Scott,et al.  Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. , 2017, Pharmacogenomics.

[8]  Victoria M. Pratt,et al.  Identification of Novel CYP2D7-2D6 Hybrids: Non-Functional and Functional Variants , 2010, Front. Pharmacol..

[9]  M. Eichelbaum,et al.  A silent mutation (2939G>A, exon 6; CYP2D6*59) leading to impaired expression and function of CYP2D6 , 2006, Pharmacogenetics and genomics.

[10]  Shufeng Zhou Polymorphism of Human Cytochrome P450 2D6 and Its Clinical Significance , 2009, Clinical pharmacokinetics.

[11]  Ulrich Broeckel,et al.  Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project. , 2016, The Journal of molecular diagnostics : JMD.

[12]  Soojin Park,et al.  Discovery of Novel Functional Variants and Extensive Evaluation of CYP2D6 Genetic Polymorphisms in Koreans , 2009, Drug Metabolism and Disposition.

[13]  Jiefu Yang,et al.  Genetic variations of human CYP2D6 in the Chinese Han population. , 2013, Pharmacogenomics.

[14]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[15]  Yao Yang,et al.  Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS) , 2015, BMC Genomics.

[16]  A. Gaedigk Complexities of CYP2D6 gene analysis and interpretation , 2013, International review of psychiatry.

[17]  Neil A. Miller,et al.  The Evolution of PharmVar , 2018, Clinical pharmacology and therapeutics.

[18]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[19]  R. Weinshilboum Inheritance and drug response. , 2003, The New England journal of medicine.

[20]  M. Whirl‐Carrillo,et al.  Prediction of CYP2D6 phenotype from genotype across world populations , 2016, Genetics in Medicine.

[21]  R. Sebra,et al.  Long‐Read Single Molecule Real‐Time Full Gene Sequencing of Cytochrome P450‐2D6 , 2016, Human mutation.

[22]  A. Gaedigk,et al.  CYP2C9*61, a rare missense variant identified in a Puerto Rican patient with low warfarin dose requirements. , 2019, Pharmacogenomics.

[23]  Greyson Twist,et al.  CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR. , 2012, Pharmacogenomics.

[24]  A. Gaedigk,et al.  CYP2D6*36 GENE ARRANGEMENTS WITHIN THE CYP2D6 LOCUS: ASSOCIATION OF CYP2D6*36 WITH POOR METABOLIZER STATUS , 2006, Drug Metabolism and Disposition.

[25]  D. Mrazek,et al.  CYP2D6: novel genomic structures and alleles , 2009, Pharmacogenetics and genomics.

[26]  C. Nofziger,et al.  Accurately genotyping CYP2D6: not for the faint of heart. , 2018, Pharmacogenomics.

[27]  Kazufumi Watanabe,et al.  Digital PCR for determination of cytochrome P450 2D6 and sulfotransferase 1A1 gene copy number variations. , 2017, Drug discoveries & therapeutics.

[28]  Elaine Lyon,et al.  Developing a Sustainable Process to Provide Quality Control Materials for Genetic Testing , 2005, Genetics in Medicine.

[29]  Bin Chen,et al.  Good laboratory practices for molecular genetic testing for heritable diseases and conditions. , 2009 .

[30]  U. Fuhr,et al.  CYP2D7-2D6 hybrid tandems: identification of novel CYP2D6 duplication arrangements and implications for phenotype prediction. , 2010, Pharmacogenomics.

[31]  Richard C. Friedberg,et al.  International Organization for Standardization (ISO) 15189 , 2017, Annals of laboratory medicine.

[32]  Barbara Zehnbauer,et al.  Characterization of 107 genomic DNA reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1: a GeT-RM and Association for Molecular Pathology collaborative project. , 2010, The Journal of molecular diagnostics : JMD.