Practical interpretation of CYP2D6 haplotypes: Comparison and integration of automated and expert calling

Clinica Chimica Acta

Volumn 456, Issue , 2016, Pages 7-14

  Ruaño, Gualberto ^a   Kocherla, Mohan ^a   Graydon, James S ^a   Holford, Theodore R ^b   Makowski, Gregory S ^c   Goethe, John W ^c  

^a Genomas Inc   (United States)

^b YALE UNIVERSITY   (United States)

^c HARTFORD HOSPITAL   (United States)

Author keywords

Buccal swab; CYP2D6 haplotyping; Gene duplications; Genotyping software; Laboratory Information System; Molecular diagnostics interpretation

Indexed keywords

CYTOCHROME P450 2D6; DNA;

ALGORITHM; ARTICLE; AUTOMATED CALLING; CONTROLLED STUDY; DNA EXTRACTION; EXPERT CALLING; FEMALE; GENE DUPLICATION; GENE LOCUS; GENETIC ANALYZER; GENOTYPING TECHNIQUE; HAPLOTYPE; HEMIZYGOTE; HOMOZYGOTE; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MALE; MOLECULAR DIAGNOSTICS; ORAL BIOPSY; POPULATION GENETICS; PRIORITY JOURNAL; SIGNAL PROCESSING; ARTIFICIAL INTELLIGENCE; AUTOMATION; COMPARATIVE STUDY; GENETICS; PROCEDURES; REPRODUCIBILITY; SOFTWARE; STATISTICAL ANALYSIS;

ARTIFICIAL INTELLIGENCE; AUTOMATION; CYTOCHROME P-450 CYP2D6; DATA INTERPRETATION, STATISTICAL; FEMALE; GENE DUPLICATION; GENOTYPING TECHNIQUES; HAPLOTYPES; HUMANS; MALE; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84959208572     PISSN: 00098981     EISSN: 18733492     Source Type: Journal    
DOI: 10.1016/j.cca.2016.02.011     Document Type: Article

References (39)

1. Kirchheiner J., Nickchen K., Bauer M., Wong M.L., Licinio J., Roots I., Brockmöller J. Pharmacogenetics of antidepressants and antipsychotics: the contribution of allelic variations to the phenotype of drug response. Mol. Psychiatry 2004, 9(5):442-473.
2. Schenk P.W., van Fessem M., Rij S.V., Mathot R.A.A., van Gelder T., Vulto A.G., van Vliet M., Lindemans J., Brujin J.A., Schaik R.H.N. Association of graded allele-specific changes in CYP2D6 function with imipramine dose requirement in a large group of depressed patients. Mol. Psychiatry 2008, 13(6):597-605.
3. Susce M.T., Murray-Carmichael E., de Leon J. Response to hydrocodone, codeine and oxycodone in a CYP2D6 poor metabolizer. Prog. Neuro-Psychopharmacol. Biol. Psychiatry 2006, 30(7):1356-1358.
4. Crews K.R., Gaedigk A., Dunnenberger H.M., Leeder J.S., Klein T.E., Caudle K.E., Haidar C.E., Shen D.D., Callaghan J.T., Sadhasivam S.S., Prows C.A., Kharasch E.D., Skaar T.C. Clinical Pharmacogenetics Implementation Consortium guidelines for cytochrome P450 2D6 genotype and codeine therapy: 2014 update. Clin. Pharmacol. Ther. 2014, 95(4):376-382.
5. Bijl M.J., Visser L.E., Van Schaik R.H.N., Kors J.A., Witteman J.C.M., Albert Hofman, Vulto A.G., van Gelder Teun, Stricker BHCh Genetic variation in the CYP2D6 gene is associated with a lower heart rate and blood pressure in β-blocker users. Clin. Pharmacol. Ther. 2009, 85(1):45-50.
6. Desta Z., Flockhart D.A. Germline pharmacogenetics of tamoxifen response: have we learned enough?. J. Clin. Oncol. 2007, 25(33):5147-5149.
7. Province M.A., Goetz M.P., Brauch H., Flockhart D.A., Hebert J.M., Whaley R., Suman V.J., Schroth W., Winter S., Zembutsu H., Mushiroda T., Newman W.G., Lee M.-T.M., Ambrosone C.B., Beckmann M.W., Choi J.-Y., Dieudonné A.-S., Fasching P.A., Ferraldeschi R., Gong L., Haschke-Becher E., Howell A., Jordan L.B., Hamann U., Kiyotani K., Krippl P., Lambrechts D., Latif A., Langsenlehner U., Lorizio W., Neven P., Nguyen A.T., Park B.-W., Purdie C.A., Quinlan P., Renner W., Schmidt M., Schwab M., Shin J.-G., Stingl J.C., Wegman P., Wingren S., Wu A.H.B., Ziv E., Zirpoli G., Thompson A.M., Jordan V.C., Nakamura Y., Altman R.B., Ames M.M., Weinshilboum R.M., Eichelbaum M., Ingle J.N., Klein T.E., International Tamoxifen Pharmacogenomics Consortium CYP2D6 genotype and adjuvant tamoxifen: Meta-Analysis of heterogeneous study populations. Clin. Pharmacol. Ther. 2014, 95(2):216-227.
8. Skierka J.M., Walker D.L., Peterson S.E., O'Kane D.J., Black J.L. CYP2D6* 11 and challenges in clinical genotyping of the highly polymorphic CYP2D6 gene. Pharmacogenomics 2012, 13(8):951-954.
9. Gaedigk A. Complexities of CYP2D6 gene analysis and interpretation. Int. Rev. Psychiatry 2013, 25(5):534-553.
10. Pratt V.M., Zehnbauer B., Wilson J.A., Baak R., Babic N., Bettinotti M., Kalman L. 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. 2010, 12(6):835-846.
11. Wu A.H. Genotype and phenotype concordance for pharmacogenetic tests through proficiency survey testing. Arch. Pathol. Lab. Med. 2013, 137(9):1232-1236.
12. de Leon J., Arranz M.J., Ruaño G. Pharmacogenetic testing in psychiatry: a review of features and clinical realities. Clin. Lab. Med. 2008, 28(4):599-617.
13. Kramer W.E., Walker D.L., O'Kane D.J., Mrazek D.A., Fisher P.K., Dukek B.A., Bruflat J.K., Black J.L. CYP2D6: novel genomic structures and alleles. Pharmacogenet. Genomics 2009, 19(10):813.
14. Black J.L., Walker D.L., O'Kane D.J., Harmandayan M. Frequency of undetected CYP2D6 hybrid genes in clinical samples: impact on phenotype prediction. Drug Metab. Dispos. 2012, 40(1):111-119.
15. Bourgey M., Lariviere M., Richer C., Sinnett D. ALG: automated genotype calling of Luminex assays. PLoS One 2011, 6(5):e19368.
16. Lee H.K., Lewis L.D., Tsongalis G.J., Schur B.C., Jannetto P.J., Wong S.H., Yeo K.T.J. Validation of a CYP2D6 genotyping panel on the NanoChip Molecular Biology Workstation. Clin. Chem. 2007, 53(5):823-828.
17. Gordon J., Merante F., Weiss S., Zastawny R. Pharmacogenetic P-450 screening using the Tag-It Universal bead-based array platform. Pharmacogenomics and Proteomics: Enabling the Practice of Personalized Medicine 2006, AACC Press, Washington, DC, USA.
18. Food and Drug Administration, 510(K) Substantial Equivalence Determination, Decision Summary, 510(K) Number: k130189, Genotype of Cytochrome P450 2D6 (CYP2D6), Luminex Molecular Diagnostics Inc. (Accessed at ). http://www.accessdata.fda.gov/cdrh_docs/reviews/K130189.pdf.
19. Løvlie R., Daly A.K., Molven A., Idle J.R., Steen V.M. Ultra-rapid metabolizers of debrisoquine: characterization and PCR-based detection of alleles with duplication of the CYP2D6 gene. FEBS Lett. 1996, 392(1):30-34.
20. Steen V.M., Andreassen O.A., Daly A.K., Tefre T., Borresen A.L., Idle J.R., Gulbrandsen A.K. Detection of the poor metabolizer-associated CYP2D6 (d) gene deletion allele by long-PCR technology. Pharmacogenet. Genomics 1995, 5(4):215-223.
21. Sim S.C., Ingelman-Sundberg M. The human cytochrome P450 (CYP) allele nomenclature website: a peer-reviewed database of CYP variants and their associated effects. Hum. Genomics 2010, 4(4):278.
22. Gaedigk A., Ryder D.L., Bradford L.D., Leeder J.S. CYP2D6 poor metabolizer status can be ruled out by a single genotyping assay for the -1584G promoter polymorphism. Clin. Chem. 2003, 49(6):1008-1011.
23. Food and Drug Administration, 510(k) Substantial Equivalence Determination, Decision Summary, 510(k) Number: k063224, Controls for assays detecting cytochrome P450 2D6 gene mutations and variants, Gentris Corporation. (Accessed at ). http://www.accessdata.fda.gov/cdrh_docs/reviews/k063224.pdf.
24. NIGMS Human Genetic Cell Repository, sponsored by the National Institute of General Medical Sciences at the Coriell Institute for Medical Research. (Accessed at and ). https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM17031&product=CC.
25. de Leon J., Susce M.T., Johnson M., Hardin M., Maw L., Shao A., Allen A.C.P., Chiafari F.A., Hillman G., Nikoloff D.M. DNA microarray technology in the clinical environment: the AmpliChip CYP450 test for CYP2D6 and CYP2C19 genotyping. CNS Spectr. 2009, 14(01):19-35.
26. Jannetto P.J., Wong S.H., Gock S.B., Laleli-Sahin E., Schur B.C., Jentzen J.M. Pharmacogenomics as molecular autopsy for postmortem forensic toxicology: genotyping cytochrome P450 2D6 for oxycodone cases. J. Anal. Toxicol. 2002, 26:438-447.
27. Marez D., Legrand M., Sabbagh N., Guidice J.L., Spire C., Lafitte J.J., Meyer U.A., Broly F. Polymorphism of the cytochrome P450 CYP2D6 gene in a European population: characterization of 48 mutations and 53 alleles, their frequencies and evolution. Pharmacogenet. Genomics 1997, 7(3):193-202.
28. Løvlie R., Daly A.K., Matre G.E., Molven A., Steen V.M. Polymorphisms in CYP2D6 duplication-negative individuals with the ultrarapid metabolizer phenotype: a role for the CYP2D6*35 allele in ultrarapid metabolism?. Pharmacogenetics 2000, 11:45-55.
29. Black J.L., O'Kane D.J., Mrazek D.A. The impact of CYP allelic variation on antidepressant metabolism: a review. Expert Opin. Drug Metab. Toxicol. 2007, 3(1):21-31.
30. Villagra D., Goethe J., Schwartz H.I., Szarek B., Kocherla M., Gorowski K., Berrezueta C., Schwartz H.I., Ruaño G. Novel drug metabolism indices for pharmacogenetic functional status based on combinatory genotyping of CYP2C9, CYP2C19 and CYP2D6 genes. Biomark. Med 2011, 5(4):427-438.
31. Wang D., Poi M.J., Sun X., Gaedigk A., Leeder J.S., Sadee W. Common CYP2D6 polymorphisms affecting alternative splicing and transcription: long-range haplotypes with two regulatory variants modulate CYP2D6 activity. Hum. Mol. Genet. 2014, 23(1):268-278.
32. Wang D., Papp A.C., Sun X. Functional characterization of CYP2D6 enhancer polymorphisms. Hum. Mol. Genet. 2015, 24(6):1556-1562.
33. Ramamoorthy A., Flockhart D.A., Hosono N., Kubo M., Nakamura Y., Skaar T.C. Differential quantification of CYP2D6 gene copy number by four different quantitative real-time PCR assays. Pharmacogenet. Genomics 2010, 20(7):451-454.
34. Melis R., Lyon E., McMillin G.A. Determination of CYP2D6, CYP2C9 and CYP2C19 genotypes with Tag-It™ mutation detection assays. Expert. Rev. Mol. Diagn. 2006, 6(6):811-820.
35. Hicks, J. K., J Swen, J., & Gaedigk, A. (2014). Challenges in CYP2D6 phenotype assignment from genotype data: a critical assessment and call for standardization. Curr. Drug Metab., 15(2), 218-232.
36. Ruaño G., Kidd K.K., Stephens J.C. Haplotype of multiple polymorphisms resolved by enzymatic amplification of single DNA molecules. Proc. Natl. Acad. Sci. U. S. A. 1990, 87(16):6296-6300.
37. Ruaño G., Kidd K.K. Genotyping and haplotyping of polymorphisms directly from genomic DNA via coupled amplification and sequencing. Nucleic Acids Res. 1991, 19:6877-6882.
38. Ruaño, G., Bentley, K. L., & Ruddle, F. H. (1999). Genome Anthologies for Harvesting DNA Variants. U.S. Patent No. 5,972,614. Washington, DC: U.S. Patent and Trademark Office.
39. Ruaño G., Blair C.L., Bower B., Windemuth A., Kocherla M., Aleman Y., Pearlson G., Goethe J.W., Schwartz H.I. Somatic complications of psychotropic medications in a patient with multiple CYP2 drug metabolism deficiencies. Conn. Med. 2007, 71(4):197-200.