253
Views
8
CrossRef citations to date
0
Altmetric
Review

Concepts Driving Pharmacogenomics Implementation Into Everyday Healthcare

ORCID Icon, ORCID Icon, & ORCID Icon
Pages 305-318 | Published online: 30 Oct 2019

References

  • Bush WS, Crosslin DR, Owusu-Obeng A, et al. Genetic variation among 82 pharmacogenes: the PGRNseq data from the eMERGE network. Clin Pharmacol Ther. 2016;100(2):160–169. doi:10.1002/cpt.35026857349
  • Ji Y, Skierka JM, Blommel JH, et al. Preemptive pharmacogenomic testing for precision medicine: a comprehensive analysis of five actionable pharmacogenomic genes using next-generation dna sequencing and a customized cyp2d6 genotyping cascade. J Mol Diagn. 2016;18(3):438–445. doi:10.1016/j.jmoldx.2016.01.00326947514
  • Van Driest SL, Shi Y, Bowton EA, et al. Clinically actionable genotypes among 10,000 patients with preemptive pharmacogenomic testing. Clin Pharmacol Ther. 2014;95(4):423–431. doi:10.1038/clpt.2013.22924253661
  • PharmGKB.org. PharmGKB dosing guidelines. 2017; Available from: https://www.pharmgkb.org/view/dosing-guidelines.do Accessed 121, 2017.
  • Weitzel KW, Elsey AR, Langaee TY, et al. Clinical pharmacogenetics implementation: approaches, successes, and challenges. Am J Med Genet C Semin Med Genet. 2014;166:56–67. doi:10.1002/ajmg.c.31390
  • Etienne-Grimaldi M-C, Boyer J-C, Thomas F, et al. UGT1A1 genotype and irinotecan therapy: general review and implementation in routine practice. Fundam Clin Pharmacol. 2015;29(3):219–237. doi:10.1111/fcp.1211725817555
  • US Food and Drug Administration. Table of pharmacogenomic biomarkers in drug labeling. 2017; Available from: http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm Accessed 1115, 2015.
  • Swen J, Nijenhuis M, de Boer A, et al. Pharmacogenetics: from bench to byte— an update of guidelines. Clin Pharmacol Ther. 2011;89(5):662–673. doi:10.1038/clpt.2011.3421412232
  • Weinshilboum RM, Wang L. Pharmacogenomics: precision medicine and drug response. Mayo Clin Proc. 2017;92(11):1711–1722. doi:10.1016/j.mayocp.2017.09.00129101939
  • Le K-Q, Prabhakar BS, Hong W-J, Li L-C. Alternative splicing as a biomarker and potential target for drug discovery. Acta Pharmacol Sin. 2015;36(10):1212–1218. doi:10.1038/aps.2015.4326073330
  • Wang D, Sadee W. CYP3A4 intronic SNP rs35599367 (CYP3A4*22) alters RNA splicing. Pharmacogenet Genomics. 2016;26(1):40–43. doi:10.1097/FPC.000000000000018326488616
  • Zanger UM, Schwab M. Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol Ther. 2013;138(1):103–141. doi:10.1016/j.pharmthera.2012.12.00723333322
  • Weinshilboum RM, Diane M, Otterness A, Szumlanski CL. Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase. Annu Rev Pharmacol Toxicol. 1999;39(1):19–52. doi:10.1146/annurev.pharmtox.39.1.1910331075
  • Wang L, Nguyen TV, McLaughlin RW, Sikkink LA, Ramirez-Alvarado M, Weinshilboum RM. Human thiopurine S-methyltransferase pharmacogenetics: variant allozyme misfolding and aggresome formation. Proc Natl Acad Sci U S A. 2005;102(26):9394. doi:10.1073/pnas.050235210215967990
  • DeLozier TC, Lee S-C, Coulter SJ, Goh BC, Goldstein JA. Functional characterization of novel allelic variants of CYP2C9 recently discovered in Southeast Asians. J Pharmacol Exp Ther. 2005;315(3):1085. doi:10.1124/jpet.105.09118116099926
  • Wang ZH, Zhan YY, Li YX, et al. Effects of 24 CYP2D6 variants found in the chinese population on the metabolism of risperidone. Pharmacology. 2015;96(5–6):290–295. doi:10.1159/00044100726544071
  • Flanagan SE, Patch A-M, Ellard S. Using SIFT and polyphen to predict loss-of-function and gain-of-function mutations. Genet Test Mol Biomarkers. 2010;14(4):533–537. doi:10.1089/gtmb.2010.003620642364
  • Devarajan S, Moon I, Ho M-F, et al. Pharmacogenomic next-generation DNA sequencing: lessons from the identification and functional characterization of variants of unknown significance in CYP2C9 and CYP2C19. Drug Metab Dispos. 2019;47(4):425.30745309
  • Guo X, Chavez A, Tung A, et al. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nat Biotechnol. 2018;36(6):540–546. doi:10.1038/nbt.414729786095
  • Trubetskoy OV, Gibson JR, Marks BD. Highly miniaturized formats for in vitro drug metabolism assays using vivid® fluorescent substrates and recombinant human cytochrome P450 enzymes. J Biomol Screen. 2005;10(1):56–66. doi:10.1177/108705710426973115695344
  • Cheng Q, Sohl CD, Guengerich FP. High-throughput fluorescence assay of cytochrome P450 3A4. Nat Protoc. 2009;4(9):1258–1261. doi:10.1038/nprot.2009.12319661996
  • Wadelius M. Warfarin pharmacogenetics: it matters if you’re black or white. Blood. 2014;124(14):2171. doi:10.1182/blood-2014-08-59411925278569
  • Kozyra M, Ingelman-Sundberg M, Lauschke VM. Rare genetic variants in cellular transporters, metabolic enzymes, and nuclear receptors can be important determinants of interindividual differences in drug response. Genet Med. 2016;19:20. doi:10.1038/gim.2016.3327101133
  • Karczewski KJ, Weisburd B, Thomas B, et al. The ExAC browser: displaying reference data information from over 60 000 exomes. Nucleic Acids Res. 2017;45(D1):D840–D845. doi:10.1093/nar/gkw97127899611
  • Lakiotaki K, Kanterakis A, Kartsaki E, Katsila T, Patrinos GP, Potamias G. Exploring public genomics data for population pharmacogenomics. PLoS One. 2017;12(8):e0182138. doi:10.1371/journal.pone.018213828771511
  • Ortega VE, Meyers DA. Pharmacogenetics: implications of race and ethnicity on defining genetic profiles for personalized medicine. J Allergy Clin Immunol. 2014;133(1):16–26. doi:10.1016/j.jaci.2013.10.04024369795
  • Hewett M, Oliver DE, Rubin DL, et al. PharmGKB: the pharmacogenetics knowledge base. Nucleic Acids Res. 2002;30(1):163–165. doi:10.1093/nar/30.1.16311752281
  • Pratt VM, Del Tredici AL, Hachad H, et al. Recommendations for clinical CYP2C19 genotyping allele selection: a report of the association for molecular pathology. J Mol Diagn. 2018;20(3):269–276. doi:10.1016/j.jmoldx.2018.01.01129474986
  • Eadon MT, Desta Z, Levy KD, et al. Implementation of a pharmacogenomics consult service to support the INGENIOUS trial. Clin Pharmacol Ther. 2016;100(1):63–66. doi:10.1002/cpt.34726850569
  • Athreya AP, Neavin D, Carrillo-Roa T, et al. Pharmacogenomics-driven prediction of antidepressant treatment outcomes: a machine learning approach with multi-trial replication. Clin Pharmacol Ther. 2019;106:855–865. doi:10.1002/cpt.v106.431012492
  • Athreya AP, Gaglio AJ, Cairns J, et al. Machine learning helps identify new drug mechanisms in triple-negative breast cancer. IEEE Trans Nanobioscience. 2018;17(3):251–259. doi:10.1109/TNB.2018.285199729994716
  • Moyer AM, Caraballo PJ. The challenges of implementing pharmacogenomic testing in the clinic. Expert Rev Pharmacoecon Outcomes Res. 2017;17(6):567–577. doi:10.1080/14737167.2017.138539528949250
  • Caraballo PJ, Bielinski SJ, St Sauver JL, Weinshilboum RM. Electronic medical record-integrated pharmacogenomics and related clinical decision support concepts. Clin Pharmacol Ther. 2017;102(2):254–264. doi:10.1002/cpt.70728390138
  • Hicks JK, Dunnenberger HM, Gumpper KF, Haidar CE, Hoffman JM. Integrating pharmacogenomics into electronic health records with clinical decision support. Am J Health Syst Pharm. 2016;73(23):1967–1976. doi:10.2146/ajhp16003027864204
  • Blagec K, Koopmann R, Crommentuijn – van Rhenen M, et al. Implementing pharmacogenomics decision support across seven European countries: the Ubiquitous Pharmacogenomics (U-PGx) project. J Am Med Inform Assoc. 2018;25(7):893–898. doi:10.1093/jamia/ocy00529444243
  • van der Wouden CH, Cambon-Thomsen A, Cecchin E, et al. Implementing pharmacogenomics in Europe: design and implementation strategy of the ubiquitous pharmacogenomics consortium. Clin Pharmacol Ther. 2017;101(3):341–358. doi:10.1002/cpt.60228027596
  • Wu RR, Myers RA, Hauser ER, et al. Impact of genetic testing and family health history based risk counseling on behavior change and cognitive precursors for type 2 diabetes. J Genet Couns. 2017;26(1):133–140. doi:10.1007/s10897-016-9988-z27296809
  • Ritchie MD, Verma SS, Hall MA, et al. Electronic medical records and genomics (eMERGE) network exploration in cataract: several new potential susceptibility loci. Mol Vis. 2014;20:1281–1295.25352737
  • Pulley JM, Denny JC, Peterson JF, et al. Operational Implementation of Prospective Genotyping for Personalized Medicine: The Design of the Vanderbilt PREDICT Project. Clin Pharmacol Ther. 2012;92(1):87–95. doi:10.1038/clpt.2011.371
  • Bielinski SJ, Olson JE, Pathak J, et al. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol. Mayo Clin Proc. 2014;89(1):25–33. doi:10.1016/j.mayocp.2013.10.02124388019
  • Bielinski SJ, St Sauver JL, Olson JE, et al. Cohort profile: the right drug, right dose, right time: using genomic data to individualize treatment protocol (RIGHT protocol). Int J Epidemiol. 2019. doi:10.1093/ije/dyz123
  • Manolio TA, Green ED. Leading the way to genomic medicine. Am J Med Genet C Semin Med Genet. 2014;166C(1):1–7. doi:10.1002/ajmg.c.3138424619573
  • Moyer AM, Rohrer Vitek CR, Giri J, Caraballo PJ. Challenges in ordering and interpreting pharmacogenomic tests in clinical practice. Am J Med. 2017;130(12):1342–1344. doi:10.1016/j.amjmed.2017.07.01228757317
  • Bousman CA, Jaksa P, Pantelis C. Systematic evaluation of commercial pharmacogenetic testing in psychiatry: a focus on CYP2D6 and CYP2C19 allele coverage and results reporting. Pharmacogenet Genomics. 2017;27(11):387–393. doi:10.1097/FPC.000000000000030328777243
  • Sangkuhl K, Whirl-Carrillo M, Whaley RM, et al. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther. 2018;104(1):19–22.29194583
  • Lee S-B, Wheeler MM, Patterson K, et al. Stargazer: a software tool for calling star alleles from next-generation sequencing data using CYP2D6 as a model. Genet Med. 2019;21(2):361–372. doi:10.1038/s41436-018-0054-029875422
  • Gandhi MJ, Ferriola D, Huang Y, Duke JL, Monos D. Targeted next-generation sequencing for human leukocyte antigen typing in a clinical laboratory: metrics of relevance and considerations for its successful implementation. Arch Pathol Lab Med. 2017;141(6):806–812. doi:10.5858/arpa.2016-0537-RA28234015
  • Bousman CA, Dunlop BW. Genotype, phenotype, and medication recommendation agreement among commercial pharmacogenetic-based decision support tools. Pharmacogenomics J. 2018;18(5):613–622. doi:10.1038/s41397-018-0027-329795409
  • Pratt VM, Cavallari LH, Del Tredici AL, et al. Recommendations for clinical CYP2C9 genotyping allele selection: a joint recommendation of the association for molecular pathology and college of american pathologists. J Mol Diagn. 2019. doi:10.1016/j.jmoldx.2019.04.003
  • Gaedigk A, Sangkuhl K, Whirl-Carrillo M, et al. The Evolution of PharmVar. Clin Pharmacol Ther. 2019;105(1):29–32. doi:10.1002/cpt.127530536702
  • Sim SC, Altman RB, Ingelman-Sundberg M. Databases in the area of pharmacogenetics. Hum Mutat. 2011;32(5):526–531. doi:10.1002/humu.2145421309040
  • Pratt VM, Everts RE, Aggarwal P, et al. Characterization of 137 genomic DNA reference materials for 28 pharmacogenetic genes: a GeT-RM collaborative project. J Mol Diagn. 2016;18(1):109–123. doi:10.1016/j.jmoldx.2015.08.00526621101
  • Pratt VM, Zehnbauer B, Wilson JA, 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. J Mol Diagn. 2010;12(6):835–846. doi:10.2353/jmoldx.2010.10009020889555
  • Wu AHB. Genotype and phenotype concordance for pharmacogenetic tests through proficiency survey testing. Arch Pathol Lab Med. 2013;137(9):1232–1236. doi:10.5858/arpa.2012-0261-CP23991737
  • Kelly MA, Caleshu C, Morales A, et al. Adaptation and validation of the ACMG/AMP variant classification framework for MYH7-associated inherited cardiomyopathies: recommendations by clingen’s inherited cardiomyopathy expert panel. Genet Med. 2018;20(3):351–359. doi:10.1038/gim.2017.21829300372
  • Moon JY, Franchi F, Rollini F, et al. Role of genetic testing in patients undergoing percutaneous coronary intervention. Expert Rev Clin Pharmacol. 2018;11(2):151–164. doi:10.1080/17512433.2017.135390928689434
  • CPIC.org. 2019; Available from: https://cpicpgx.org/guidelines/ Accessed 71, 2019.
  • Johansen Taber KA, Dickinson BD. Pharmacogenomic knowledge gaps and educational resource needs among physicians in selected specialties. Pharmgenomics Pers Med. 2014;7:145–162. doi:10.2147/PGPM25045280
  • Maciel A, Cullors A, Lukowiak AA, Garces J. Estimating cost savings of pharmacogenetic testing for depression in real-world clinical settings. Neuropsychiatr Dis Treat. 2018;14:225–230. doi:10.2147/NDT.S14504629386895
  • Myriad genetics genesight pgx test garners UnitedHealthcare coverage. Genomeweb 2019.
  • Keeling NJ, Rosenthal MM, West-Strum D, Patel AS, Haidar CE, Hoffman JM. Preemptive pharmacogenetic testing: exploring the knowledge and perspectives of US payers. Genet Med. 2017. doi:10.1038/gim.2017.1181.
  • USFDA.org. FDA authorizes first direct-to-consumer test for detecting genetic variants that may be associated with medication metabolism. 2019; Available from: https://www.fda.gov/news-events/press-announcements/fda-authorizes-first-direct-consumer-test-detecting-genetic-variants-may-be-associated-medication Accessed 625, 2019.
  • Rosenblat JD, Lee Y, McIntyre RS. Does pharmacogenomic testing improve clinical outcomes for major depressive disorder? A systematic review of clinical trials and cost-effectiveness studies. J Clin Psychiatry. 2017;78(6):720–729. doi:10.4088/JCP.15r1058328068459
  • Goldberg JF. Do you order pharmacogenetic testing? Why? J Clin Psychiatry. 2017;78(8):1155–1156. doi:10.4088/JCP.17ac1181328796939
  • Haga SB, Burke W, Ginsburg GS, Mills R, Agans R. Primary care physicians’ knowledge of and experience with pharmacogenetic testing. Clin Genet. 2012;82(4):388–394. doi:10.1111/j.1399-0004.2012.01908.x22698141
  • Formea CM, Nicholson WT, McCullough KB, et al. Development and evaluation of a pharmacogenomics educational program for pharmacists. Am J Pharm Educ. 2013;77(1):10. doi:10.5688/ajpe77816623459098
  • Haga SB, Mills R. Nurses’ communication of pharmacogenetic test results as part of discharge care. Pharmacogenomics. 2015;16(3):251–256. doi:10.2217/pgs.14.17325712188
  • Roden DM, Altman RB, Benowitz NL, et al. Pharmacogenomics: challenges and opportunities. Ann Intern Med. 2006;145(10):749–757. doi:10.7326/0003-4819-145-10-200611210-0000717116919
  • Giri J, Curry TB, Formea CM, Nicholson WT, Rohrer Vitek CR. Education and knowledge in pharmacogenomics: still a challenge? Clin Pharmacol Ther. 2018;103(5):752–755. doi:10.1002/cpt.101929417560
  • Unertl KM, Jaffa H, Field JR, Price L, Peterson JF. Clinician perspectives on using pharmacogenomics in clinical practice. Per Med. 2015;12(4):339–347. doi:10.2217/pme.15.1026635887
  • Roederer MW, Kuo GM, Kisor DF, et al. Pharmacogenomics competencies in pharmacy practice: a blueprint for change. J Am Pharm Assoc (2003). 2017;57(1):120–125. doi:10.1016/j.japh.2016.08.01427816542
  • Higgs JE, Andrews J, Gurwitz D, Payne K, Newman W. Pharmacogenetics education in British medical schools. Genomic Med. 2008;2(3–4):101–105. doi:10.1007/s11568-009-9032-619363698
  • Swen JJ, Huizinga TW, Gelderblom H, et al. Translating pharmacogenomics: challenges on the road to the clinic. PLoS Med. 2007;4(8):e209. doi:10.1371/journal.pmed.004020917696640
  • Ross CJ, Visscher H, Sistonen J, et al. The Canadian pharmacogenomics network for drug safety: a model for safety pharmacology. Thyroid. 2010;20(7):681–687. doi:10.1089/thy.2010.164220578893
  • Klein TE, Ritchie MD. PharmCAT: a pharmacogenomics clinical annotation tool. Clin Pharmacol Ther. 2018;104(1):19–22. doi:10.1002/cpt.92829194583
  • Bank PCD, Swen JJ, Schaap RD, Klootwijk DB, Baak – Pablo R, Guchelaar H-J. A pilot study of the implementation of pharmacogenomic pharmacist initiated pre-emptive testing in primary care. Eur J Hum Genet. 2019;27(10):1532–1541. doi:10.1038/s41431-019-0454-x31227807