Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project

Journal of Molecular Diagnostics

Volumn 18, Issue 1, 2016, Pages 109-123

  Pratt, Victoria M ^a   Everts, Robin E ^b   Aggarwal, Praful ^c   Beyer, Brittany N ^a   Broeckel, Ulrich ^c   Epstein Baak, Ruth ^d   Hujsak, Paul ^d   Kornreich, Ruth ^e   Liao, Jun ^e   Lorier, Rachel ^c   Scott, Stuart A ^e   Smith, Chingying Huang ^d   Toji, Lorraine H ^f   Turner, Amy ^c   Kalman, Lisa V ^g  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b AGENA BIOSCIENCE   (United States)

^c MEDICAL COLLEGE OF WISCONSIN   (United States)

^d AutoGenomics Inc   (United States)

^e MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^f Laboratory of Molecular and Cellular Biology of Hematopoiesis   (United States)

^g CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 1A1; CYTOCHROME P450 1A2; CYTOCHROME P450 2A6; CYTOCHROME P450 2B6; CYTOCHROME P450 2C19; CYTOCHROME P450 2C8; CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; CYTOCHROME P450 2E1; CYTOCHROME P450 3A4; CYTOCHROME P450 3A5; CYTOCHROME P450 4F2; GENOMIC DNA; GLUCURONOSYLTRANSFERASE 1A1; GLUCURONOSYLTRANSFERASE 2B15; GLUCURONOSYLTRANSFERASE 2B17; GLUCURONOSYLTRANSFERASE 2B7; GLUTATHIONE TRANSFERASE M1; GLUTATHIONE TRANSFERASE P1; GLUTATHIONE TRANSFERASE T1; NAT2 PROTEIN; NORADRENALIN TRANSPORTER; ORGANIC ANION TRANSPORTER B; ORGANIC CATION TRANSPORTER 2; PEPTIDE TRANSPORTER 2; SOLUTE CARRIER ORGANIC ANION TRANSPORTER 1B1; TPMT PROTEIN; UNCLASSIFIED DRUG; VKORC1 PROTEIN; CARRIER PROTEIN; CYTOCHROME P450; GLUCURONOSYLTRANSFERASE; GLUTATHIONE TRANSFERASE;

ALLELE; ARTICLE; CLINICAL LABORATORY; DISEASE CONTROL; DNA SEQUENCE; GENE NOMENCLATURE; GENETIC ANALYSIS; GENETIC SCREENING; HUMAN; HUMAN CELL; NEXT GENERATION SEQUENCING; PHARMACOGENETICS; PROPHYLAXIS; QUALITY CONTROL; ADVERSE DRUG REACTION; CELL LINE; GENETICS; GENOTYPE; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE SEQUENCE; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

BASE SEQUENCE; CARRIER PROTEINS; CELL LINE; CYTOCHROME P-450 ENZYME SYSTEM; DRUG-RELATED SIDE EFFECTS AND ADVERSE REACTIONS; GENETIC TESTING; GENOTYPE; GENOTYPING TECHNIQUES; GLUCURONOSYLTRANSFERASE; GLUTATHIONE TRANSFERASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 84954064957     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2015.08.005     Document Type: Article

References (26)

1. P.A. Gladding Clinical applications of pharmacogenetics: present and near future Cleve Clin J Med 80 2013 477 482
2. S. Ross, S.S. Anand, P. Joseph, and G. Pare Promises and challenges of phamacogenetics: an overview of study design, methodological and statistical issues JRSM Cardiovasc Dis 1 2012
3. International Organization for Standardization ISO 15189 Medical Laboratories: requirements for quality and competence 2012 International Organization for Standardization Geneva
4. Centers for Medicare and Medicaid Services, US Department of Health and Human Services. Part 493 - Laboratory Requirements: Clinical Laboratory Improvement Amendments of 1988
5. B. Chen, C.D. O'Connell, D.J. Boone, J.A. Amos, J.C. Beck, M.M. Chan, and et al. Developing a sustainable process to provide quality control materials for genetic testing Genet Med 7 2005 534 549
6. Association for Molecular Pathology statement: recommendations for in-house development and operation of molecular diagnostic tests Am J Clin Pathol 111 1999 449 463
7. Centers for Disease Control and Prevention Good laboratory practices for molecular genetic testing for heritable diseases and conditions MMWR Recomm Rep 58 RR-6 2009 1 37
8. Clinical and Laboratory Standards Institute Molecular methods for clinical genetics and oncology testing; Approved Guideline-Third Edition MM01-A3 2012 Clinical and Laboratory Standards Institute Wayne, PA
9. MM17-A Verification and validation of multiplex nucleic acid assays-Approved Guideline 2008 The Clinical and Laboratory Standards Institute (CLSI) Wayne, PA
10. V.M. Pratt, B. Zehnbauer, J. Amos Wilson, R. Baak, N. Babic, M. Bettinotti, A. Buller, K. Butz, M. Campbell, C. Civalier, A. El-Badry, D.H. Farkas, E. Lyon, S. Mandal, J. McKinney, K. Muralidharan, L. Noll, T. Sander, J. Shabbeer, C. Smith, M. Telatar, L. Toji, A. Vairavan, C. Vance, K.E. Weck, A.H.B. Wu, K.-T.J. Yeo, M. Zeller, and L. Kalman Characterization of 107 genomic DNA reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1 and UGT1A1: a GeT-RM and Association for Molecular Pathology collaborative project J Mol Diagn 12 2010 835 846
11. H. Fang, X. Liu, J. Ramírez, N. Choudhury, M. Kubo, H.K. Im, A. Konkashbaev, N.J. Cox, M.J. Ratain, Y. Nakamura, and P.H. O'Donnell Establishment of CYP2D6 reference samples by multiple validated genotyping platforms Pharmacogenomics J 14 2014 564 572
12. M.V. Relling, and T.E. Klein CPIC: clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network Clin Pharmacol Ther 89 2011 464 467
13. S.A. Miller, D.D. Dykes, and H.F. Polesky A simple salting out procedure for extracting DNA from human nucleated cells Nucleic Acids Res 16 1988 1215
14. P. Gladding, H. White, J. Voss, J. Ormiston, J. Stewart, P. Ruygrok, B. Bvaldivia, R. Baak, C. White, and M. Webster Pharmacogenetic testing for clopidogrel using the rapid INFINITI Analyzer: a dose-escalation study JACC Cardiovasc Interv 11 2009 1095 1101
15. S. Martis, I. Peter, J.S. Hulot, R. Kornreich, R.J. Desnick, and S.A. Scott Multi-ethnic distribution of clinically relevant CYP2C genotypes and haplotypes Pharmacogenomics J 13 2013 369 377
16. V.M. Pierce, and R.L. Hodinka Comparison of the GenMark Diagnostics eSensor respiratory viral panel to real-time PCR for detection of respiratory viruses in children J Clin Microbiol 50 2012 3458 3465
17. C.C. Lee, G.A. McMillin, N. Babic, R. Melis, and K.T. Yeo Evaluation of a CYP2C19 genotype panel on the GenMark eSensor® platform and the comparison to the Autogenomics Infiniti™ and Luminex CYP2C19 panels Clin Chim Acta 412 2011 1133 1137
18. K.J. Livak Allelic discrimination using fluorogenic probes and the 5' nuclease assay Genet Anal 14 1999 143 149
19. R. Melis, E. Lyon, and G.A. McMillin Determination of CYP2D6, CYP2C9 and CYP2C19 genotypes with Tag-It mutation detection assays Expert Rev Mol Diagn 6 2006 811 820
20. S.A. Scott, L. Edelmann, R. Kornreich, M. Erazo, and R.J. Desnick CYP2C9, CYP2C19 and CYP2D6 allele frequencies in the Ashkenazi Jewish population Pharmacogenomics 8 2007 721 730
21. T.Y. Langaee, H.J. Zhu, X. Wang, N. El Rouby, J.S. Markowitz, J.A. Goldstein, and J.A. Johnson The influence of the CYP2C19∗10 allele on clopidogrel activation and CYP2C19∗2 genotyping Pharmacogenet Genomics 24 2014 381 386
22. S.A. Scott, S. Martis, I. Peter, Y. Kasai, R. Kornreich, and R.J. Desnick Identification of CYP2C19∗4B: pharmacogenetic implications for drug metabolism including clopidogrel responsiveness Pharmacogenomics J 12 2012 297 305
23. A.H.B. Wu Genotype and Phenotype Concordance for Pharmacogenetic Tests Through Proficiency Survey Testing Arch Pathol Lab Med 137 2013 1232 1236
24. J.D. Robarge, L. Li, Z. Desta, A. Nguyen, and D.A. Flockhart The star-allele nomenclature: retooling for translational genomics Clin Pharmacol Ther 82 2007 244 248
25. A. Gaedigk, L. Ndjountché, K. Divakaran, L. Dianne Bradford, I. Zineh, T.F. Oberlander, D.C. Brousseau, D.G. McCarver, J.A. Johnson, S.W. Alander, K. Wayne Riggs, and J. Steven Leeder Cytochrome P4502D6 (CYP2D6) gene locus heterogeneity: characterization of gene duplication events Clin Pharmacol Ther 81 2007 242 251
26. L. Kalman, J. Agúndez, M.L. Appell, J. Black, G. Bell, and S. Boukouvala Pharmacogenetic allele nomenclature: international workgroup recommendations for test result reporting Clin Pharmacol Ther 2015 [in press] doi: 10.1002/cpt.280