Skip to main content

Pharmacogenomics: Success and Challenges

  • Chapter
  • First Online:
Genomic Applications in Pathology

Abstract

Pharmacogenomics is a field of study that explores the impact of genetic variation on pharmacokinetics and pharmacodynamics, with the goal of rational therapeutic selection. The past decade has brought together substantial advances in human genomic analysis and a maturation of our understanding of tumor biology. While there is much progress still to be had, there are now several prominent examples in which tumor-associated somatic mutations have been used to identify cellular signaling pathways in tumors. This in turn has led to the development of targeted therapies, with somatic mutations serving as genomic predictors of tumor response and providing new leads for drug development. There is also a realization that germline DNA variants can help optimize drug dosing and predict the susceptibility of patients to the adverse side effects of these drugs, knowledge that ultimately can be used to improve the benefit: risk ratio of therapeutics for individual patients.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Relling MV, Evans WE. Pharmacogenomics in the clinic. Nature. 2015;526(7573):343–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Zhang G, Nebert DW. Personalized medicine: genetic risk prediction of drug response. Pharmacol Ther. 2017;175:75–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Weinshilboum R, Wang L. Pharmacogenomics: bench to bedside. Discov Med. 2005;5(25):30–6.

    PubMed  Google Scholar 

  4. Wang L, McLeod HL, Weinshilboum RM. Genomics and drug response. N Engl J Med. 2011;364(12):1144–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lehmann H, Ryan E. The familial incidence of low pseudocholinesterase level. Lancet. 1956;271(6934):124.

    Article  CAS  PubMed  Google Scholar 

  6. Meyer UA. Pharmacogenetics and adverse drug reactions. Lancet. 2000;356(9242):1667–71.

    Article  CAS  PubMed  Google Scholar 

  7. Stearns V, et al. Active tamoxifen metabolite plasma concentrations after coadministration of tamoxifen and the selective serotonin reuptake inhibitor paroxetine. J Natl Cancer Inst. 2003;95(23):1758–64.

    Article  CAS  PubMed  Google Scholar 

  8. Kelly CM, et al. Selective serotonin reuptake inhibitors and breast cancer mortality in women receiving tamoxifen: a population based cohort study. BMJ. 2010;340:c693.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Cancer Genome Atlas Research Network. Electronic address, w.b.e. and N. Cancer Genome Atlas Research. Comprehensive and integrative genomic characterization of hepatocellular carcinoma. Cell. 2017;169(7):1327–1341 e23.

    Article  CAS  Google Scholar 

  10. Cancer Genome Atlas Research N, et al. Integrated genomic and molecular characterization of cervical cancer. Nature. 2017;543(7645):378–84.

    Google Scholar 

  11. Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015;517(7536):576–82.

    Article  CAS  Google Scholar 

  12. Cancer Genome Atlas Research N. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455(7216):1061–8.

    Article  CAS  Google Scholar 

  13. Weng L, et al. Pharmacogenetics and pharmacogenomics: a bridge to individualized cancer therapy. Pharmacogenomics. 2013;14(3):315–24.

    Article  CAS  PubMed  Google Scholar 

  14. United States Food and Drug Administration. Table of Pharmacogenomic Biomarkers in Drug Labeling.https://www.fda.gov/Drugs/ScienceResearch/ucm572698.htm./Last updated 8/3/2018.

    Google Scholar 

  15. M. Whirl-Carrillo, et al. “Pharmacogenomics Knowledge for Personalized Medicine” Clinical Pharmacology & Therapeutics (2012) 92(4):414–17.

    Google Scholar 

  16. Lee JW, et al. The emerging era of pharmacogenomics: current successes, future potential, and challenges. Clin Genet. 2014;86(1):21–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lee SY, McLeod HL. Pharmacogenetic tests in cancer chemotherapy: what physicians should know for clinical application. J Pathol. 2011;223(1):15–27.

    Article  CAS  PubMed  Google Scholar 

  18. Pratz KW, Levis M. How I treat FLT3-mutated AML. Blood. 2017;129(5):565–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Chapman PB, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Soverini S, et al. BCR-ABL kinase domain mutation analysis in chronic myeloid leukemia patients treated with tyrosine kinase inhibitors: recommendations from an expert panel on behalf of European LeukemiaNet. Blood. 2011;118(5):1208–15.

    Article  CAS  PubMed  Google Scholar 

  21. Fujii T, et al. Targeting isocitrate dehydrogenase (IDH) in cancer. Discov Med. 2016;21(117):373–80.

    PubMed  Google Scholar 

  22. Pui CH, Evans WE. A 50-year journey to cure childhood acute lymphoblastic leukemia. Semin Hematol. 2013;50(3):185–96.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Vici P, et al. Outcomes of HER2-positive early breast cancer patients in the pre-trastuzumab and trastuzumab eras: a real-world multicenter observational analysis. The RETROHER study. Breast Cancer Res Treat. 2014;147(3):599–607.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Xu ZQ, et al. Efficacy and safety of lapatinib and trastuzumab for HER2-positive breast cancer: a systematic review and meta-analysis of randomised controlled trials. BMJ Open. 2017;7(3):e013053.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Denduluri N, et al. Selection of optimal adjuvant chemotherapy regimens for human epidermal growth factor receptor 2 (HER2) -negative and adjuvant targeted therapy for HER2-positive breast cancers: an American Society of Clinical Oncology Guideline Adaptation of the Cancer Care Ontario Clinical Practice Guideline. J Clin Oncol. 2016;34(20):2416–27.

    Article  CAS  PubMed  Google Scholar 

  26. Braggio E, et al. Lessons from next-generation sequencing analysis in hematological malignancies. Blood Cancer J. 2013;3:e127.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Dewitt ND, Yaffe MP, Trounson A. Building stem-cell genomics in California and beyond. Nat Biotechnol. 2012;30(1):20–5.

    Article  CAS  PubMed  Google Scholar 

  28. Arranz EE, et al. Gene signatures in breast cancer: current and future uses. Transl Oncol. 2012;5(6):398–403.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Cancer Genome Atlas Research N. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012;489(7417):519–25.

    Article  CAS  Google Scholar 

  30. Cancer Genome Atlas N. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330–7.

    Article  CAS  Google Scholar 

  31. Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.

    Article  CAS  Google Scholar 

  32. Lipson D, et al. Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies. Nat Med. 2012;18(3):382–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Goodman AM, Choi M, Wieduwilt M, Mulroney C, Costello C, Frampton G, Miller V, Kurzrock R. Next-generation sequencing reveals potentially actionable alterations in the majority of patients with lymphoid malignancies. JCO Precis Oncol. 2017;1:1–13.

    PubMed  Google Scholar 

  34. Muller KE, et al. Targeted next-generation sequencing detects a high frequency of potentially actionable mutations in metastatic breast cancers. Exp Mol Pathol. 2016;100(3):421–5.

    Article  CAS  PubMed  Google Scholar 

  35. Vasan N, et al. A targeted next-generation sequencing assay detects a high frequency of therapeutically targetable alterations in primary and metastatic breast cancers: implications for clinical practice. Oncologist. 2014;19(5):453–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Blumenthal DT, et al. Clinical utility and treatment outcome of comprehensive genomic profiling in high grade glioma patients. J Neuro-Oncol. 2016;130(1):211–9.

    Article  CAS  Google Scholar 

  37. Rankin A, et al. Broad detection of alterations predicted to confer lack of benefit from EGFR antibodies or sensitivity to targeted therapy in advanced colorectal cancer. Oncologist. 2016;21:1306.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hagemann IS, et al. Diagnostic yield of targeted next generation sequencing in various cancer types: an information-theoretic approach. Cancer Genet. 2015;208(9):441–7.

    Article  CAS  PubMed  Google Scholar 

  39. da Cunha Santos G, Shepherd FA, Tsao MS. EGFR mutations and lung cancer. Annu Rev Pathol. 2011;6:49–69.

    Article  CAS  PubMed  Google Scholar 

  40. Paez JG, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004;304(5676):1497–500.

    Article  CAS  PubMed  Google Scholar 

  41. Kreso A, et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science. 2013;339(6119):543–8.

    Article  CAS  PubMed  Google Scholar 

  42. Amado RG, et al. Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J Clin Oncol. 2008;26(10):1626–34.

    Article  CAS  PubMed  Google Scholar 

  43. Abramson, R. 2018. Overview of Targeted Therapies for Cancer. My Cancer Genome https://www.mycancergenome.org/content/molecular-medicine/overview-of-targeted-therapies-for-cancer/ (Updated May 25).

  44. Engstrom PF, et al. NCCN molecular testing white paper: effectiveness, efficiency, and reimbursement. J Natl Compr Cancer Netw. 2011;9(Suppl 6):S1–16.

    Google Scholar 

  45. Walter MJ, et al. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. Leukemia. 2013;27(6):1275–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Walter MJ, et al. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med. 2012;366(12):1090–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Jacoby MA, Duncavage EJ, Walter MJ. Implications of tumor clonal heterogeneity in the era of next-generation sequencing. Trends Cancer. 2015;1(4):231–41.

    Article  PubMed  Google Scholar 

  48. Hussaini M. Biomarkers in hematological malignancies: a review of molecular testing in hematopathology. Cancer Control. 2015;22(2):158–66.

    Article  PubMed  Google Scholar 

  49. Cancer Genome Atlas Research N, et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059–74.

    Google Scholar 

  50. Velizheva NP, et al. Cytology smears as excellent starting material for next-generation sequencing-based molecular testing of patients with adenocarcinoma of the lung. Cancer Cytopathol. 2017;125(1):30–40.

    Article  CAS  PubMed  Google Scholar 

  51. Berg JS, et al. An informatics approach to analyzing the incidentalome. Genet Med. 2013;15(1):36–44.

    Article  CAS  PubMed  Google Scholar 

  52. Zhou SF, et al. Clinical pharmacogenetics and potential application in personalized medicine. Curr Drug Metab. 2008;9(8):738–84.

    Article  CAS  PubMed  Google Scholar 

  53. Investigators G, Investigators M, Investigators SD. Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. Am J Psychiatry. 2013;170(2):207–17.

    Article  Google Scholar 

  54. Tansey KE, et al. Contribution of common genetic variants to antidepressant response. Biol Psychiatry. 2013;73(7):679–82.

    Article  CAS  PubMed  Google Scholar 

  55. Reynolds GP. The pharmacogenetics of symptom response to antipsychotic drugs. Psychiatry Investig. 2012;9(1):1–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Drozda K, Muller DJ, Bishop JR. Pharmacogenomic testing for neuropsychiatric drugs: current status of drug labeling, guidelines for using genetic information, and test options. Pharmacotherapy. 2014;34(2):166–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Hicks JK, et al. Clinical Pharmacogenetics Implementation Consortium guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants. Clin Pharmacol Ther. 2013;93(5):402–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Leckband SG, et al. Clinical Pharmacogenetics Implementation Consortium guidelines for HLA-B genotype and carbamazepine dosing. Clin Pharmacol Ther. 2013;94(3):324–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Berinstein E, Levy A. Recent developments and future directions for the use of pharmacogenomics in cardiovascular disease treatments. Expert Opin Drug Metab Toxicol. 2017;13(9):973–83.

    Article  CAS  PubMed  Google Scholar 

  60. Giudicessi JR, Kullo IJ, Ackerman MJ. Precision cardiovascular medicine: state of genetic testing. Mayo Clin Proc. 2017;92(4):642–62.

    Article  PubMed  Google Scholar 

  61. Aceti A. Pharmacogenomics for infectious diseases. J MedMicrob Diagn. 2016;5:e223.

    Google Scholar 

  62. Young B, et al. First large, multicenter, open-label study utilizing HLA-B*5701 screening for abacavir hypersensitivity in North America. AIDS. 2008;22(13):1673–5.

    Article  CAS  PubMed  Google Scholar 

  63. Soon-U LL, Amur S. Chapter 12: “Pharmacogenomics and pharmacogenetics for infectious diseases.” in Pharmacogenomics: an introduction and clinical perspective. McGraw Hill, New York, NY, USA. 2013.

    Google Scholar 

  64. Adams JU. Pharmacogenomics and personalized medicine. Nat Educ. 2008;1:194.

    Google Scholar 

  65. Daly AK. Pharmacogenomics of adverse drug reactions. Genome Med. 2013;5(1):5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Dong Y, et al. Analysis of genetic variations in CYP2C9, CYP2C19, CYP2D6 and CYP3A5 genes using oligonucleotide microarray. Int J Clin Exp Med. 2015;8(10):18917–26.

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Eechoute K, et al. A long-term prospective population pharmacokinetic study on imatinib plasma concentrations in GIST patients. Clin Cancer Res. 2012;18(20):5780–7.

    Article  CAS  PubMed  Google Scholar 

  68. Ma Q, Lu AY. Pharmacogenetics, pharmacogenomics, and individualized medicine. Pharmacol Rev. 2011;63(2):437–59.

    Article  CAS  PubMed  Google Scholar 

  69. Ahmad A, et al. Endoxifen, a new cornerstone of breast cancer therapy: demonstration of safety, tolerability, and systemic bioavailability in healthy human subjects. Clin Pharmacol Ther. 2010;88(6):814–7.

    Article  CAS  PubMed  Google Scholar 

  70. Hertz DL, McLeod HL, Irvin WJ Jr. Tamoxifen and CYP2D6: a contradiction of data. Oncologist. 2012;17(5):620–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Irvin WJ Jr, et al. Genotype-guided tamoxifen dosing increases active metabolite exposure in women with reduced CYP2D6 metabolism: a multicenter study. J Clin Oncol. 2011;29(24):3232–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Walko CM, McLeod H. Use of CYP2D6 genotyping in practice: tamoxifen dose adjustment. Pharmacogenomics. 2012;13(6):691–7.

    Article  CAS  PubMed  Google Scholar 

  73. Baldwin RM, et al. A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101. Clin Cancer Res. 2012;18(18):5099–109.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Hertz DL, et al. CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel. Breast Cancer Res Treat. 2012;134(1):401–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Ross CJ, et al. Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy. Nat Genet. 2009;41(12):1345–9.

    Article  CAS  PubMed  Google Scholar 

  76. Visscher H, et al. Pharmacogenomic prediction of anthracycline-induced cardiotoxicity in children. J Clin Oncol. 2012;30(13):1422–8.

    Article  PubMed  Google Scholar 

  77. McWhinney SR, Goldberg RM, McLeod HL. Platinum neurotoxicity pharmacogenetics. Mol Cancer Ther. 2009;8(1):10–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Peters EJ, et al. Pharmacogenomic characterization of US FDA-approved cytotoxic drugs. Pharmacogenomics. 2011;12(10):1407–15.

    Article  CAS  PubMed  Google Scholar 

  79. McLeod HL. Cancer pharmacogenomics: early promise, but concerted effort needed. Science. 2013;339(6127):1563–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Cox NJ, et al. Clinical translation of cell-based pharmacogenomic discovery. Clin Pharmacol Ther. 2012;92(4):425–7.

    Article  CAS  PubMed  Google Scholar 

  81. Weinshilboum RM, Wang L. Pharmacogenomics: precision medicine and drug response. Mayo Clin Proc. 2017;92(11):1711–22.

    Article  CAS  PubMed  Google Scholar 

  82. Ratain MJ, et al. The cancer and leukemia group B pharmacology and experimental therapeutics committee: a historical perspective. Clin Cancer Res. 2006;12(11 Pt 2):3612s–6s.

    Article  CAS  PubMed  Google Scholar 

  83. Innocenti F, et al. A genome-wide association study of overall survival in pancreatic cancer patients treated with gemcitabine in CALGB 80303. Clin Cancer Res. 2012;18(2):577–84.

    Article  CAS  PubMed  Google Scholar 

  84. Relling MV, Klein TE. CPIC: clinical pharmacogenetics implementation consortium of the pharmacogenomics research network. Clin Pharmacol Ther. 2011;89(3):464–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Hicks JK, et al. Patient decisions to receive secondary pharmacogenomic findings and development of a multidisciplinary practice model to integrate results into patient care. Clin Transl Sci. 2018;11(1):71–6.

    Article  PubMed  Google Scholar 

  86. Hicks JK, et al. Clinical pharmacogenetics implementation consortium guideline (CPIC) for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants: 2016 update. Clin Pharmacol Ther. 2016;102:37.

    Article  Google Scholar 

  87. Saldivar JS, et al. Initial assessment of the benefits of implementing pharmacogenetics into the medical management of patients in a long-term care facility. Pharmgenomics Pers Med. 2016;9:1–6.

    PubMed  PubMed Central  Google Scholar 

  88. Lopez-Lopez E, et al. Polymorphisms of the SLCO1B1 gene predict methotrexate-related toxicity in childhood acute lymphoblastic leukemia. Pediatr Blood Cancer. 2011;57(4):612–9.

    Article  PubMed  Google Scholar 

  89. Wheeler HE, et al. Cancer pharmacogenomics: strategies and challenges. Nat Rev Genet. 2013;14(1):23–34.

    Article  CAS  PubMed  Google Scholar 

  90. van Staveren MC, et al. Evaluation of predictive tests for screening for dihydropyrimidine dehydrogenase deficiency. Pharmacogenomics J. 2013;13(5):389–95.

    Article  CAS  PubMed  Google Scholar 

  91. Kalia M. Biomarkers for personalized oncology: recent advances and future challenges. Metabolism. 2015;64(3 Suppl 1):S16–21.

    Article  CAS  PubMed  Google Scholar 

  92. Patil SA, et al. Novel approaches to glioma drug design and drug screening. Expert Opin Drug Discovery. 2013;8(9):1135–51.

    Article  CAS  Google Scholar 

  93. Ranieri G, et al. Vascular endothelial growth factor (VEGF) as a target of bevacizumab in cancer: from the biology to the clinic. Curr Med Chem. 2006;13(16):1845–57.

    Article  CAS  PubMed  Google Scholar 

  94. Konstantinopoulos PA, et al. Gene expression profile of BRCAness that correlates with responsiveness to chemotherapy and with outcome in patients with epithelial ovarian cancer. J Clin Oncol. 2010;28(22):3555–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Howard L. McLeod .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Hussaini, M.O., McLeod, H.L. (2019). Pharmacogenomics: Success and Challenges. In: Netto, G., Kaul, K. (eds) Genomic Applications in Pathology. Springer, Cham. https://doi.org/10.1007/978-3-319-96830-8_38

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-96830-8_38

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-96829-2

  • Online ISBN: 978-3-319-96830-8

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics