Pharmacogenomics and Stratified Healthcare

BIOL67481 Pharmacogenomics and Stratified Healthcare 15 Semester 1 Postgraduate Taught Level 7 William Newman Unit coordinator 1 FHEQ level (Framework for Higher Education Qualifications) ' Masters/Integrated Masters P4 ' European Credit Transfer & Accumulation System Rating : 7.5 <div>Pharmacogenomics and Stratified Healthcare  Pharmacogenomics (PGx) is defined by the Food and Drug Administration (FDA) as: "The study of variations of DNA and RNA characteristics as related to drug response". PGx is utilised in two main areas:  (a) To inform the drug development process and  (b) To help inform personalised prescribing and/or the stratification of patients into sub-groups  In both cases, PGx focuses on the predictive outcome of drug interventions. This may involve the utilisation of companion diagnostics (CDx) alongside drug therapeutic treatment. A typical CDx might be a molecular assay that, for instance, measures specific mutations to stratify sub-populations, select appropriate medication or tailor dosages to a patient's specific needs.  PGx has the potential to change healthcare significantly, since differences between patients' response to treatment can be partially explained by their genotype (pharmacokinetic, pharmacodynamic, and immunological genetic variability). Using PGx data alongside other clinical information can be used to develop individualised or stratified healthcare for patients. It may also contribute towards a more effective and safer use of drugs, potentially decreasing costs, resulting from drug toxicity and lack of efficacy, by identifying patients most likely to respond positively to a particular drug at a particular dose.  Indicative Content  1. Genomic basis of drug response including: drug mechanisms of action, drug  effectiveness and drug toxicity, including: pharmacokinetics, pharmacodynamics and  immune hypersensitivity responses, discussing ethnic differences and how these  are/might be applied in prescribing practice.  2. Use of genomic information, for targeted drug development with particular emphasis on the genes encoding metabolic enzymes, drug transporters and drug receptors and drug:drug interactions  3. Companion diagnostics and NHS service delivery models  4. Different types and examples of genomic-targeted intervention (examples of genomically-targeted clinical, therapeutic or lifestyle choices) 5. Genomic biomarkers and genetic polymorphisms leading to inter-individual variability in drug response: SNPs, short sequence repeats, haplotypes, DNA epigenetic modifications, e.g. methylation, deletions or insertions, copy number variants, RNA expression levels, RNA splicing, microRNA levels  6. Use of biomarkers and genetic testing in treatments other than cancer   </div>  <div>Pharmacogenomics and Stratified Healthcare  Pharmacogenomics (PGx) is defined by the Food and Drug Administration (FDA) as: "The study of variations of DNA and RNA characteristics as related to drug response". PGx is utilised in two main areas:  (a) To inform the drug development process and  (b) To help inform personalised prescribing and/or the stratification of patients into sub-groups  In both cases, PGx focuses on the predictive outcome of drug interventions. This may involve the utilisation of companion diagnostics (CDx) alongside drug therapeutic treatment. A typical CDx might be a molecular assay that, for instance, measures specific mutations to stratify sub-populations, select appropriate medication or tailor dosages to a patient's specific needs.  PGx has the potential to change healthcare significantly, since differences between patients' response to treatment can be partially explained by their genotype (pharmacokinetic, pharmacodynamic, and immunological genetic variability). Using PGx data alongside other clinical information can be used to develop individualised or stratified healthcare for patients. It may also contribute towards a more effective and safer use of drugs, potentially decreasing costs, resulting from drug toxicity and lack of efficacy, by identifying patients most likely to respond positively to a particular drug at a particular dose.  Indicative Content  1. Genomic basis of drug response including: drug mechanisms of action, drug  effectiveness and drug toxicity, including: pharmacokinetics, pharmacodynamics and  immune hypersensitivity responses, discussing ethnic differences and how these  are/might be applied in prescribing practice.  2. Use of genomic information, for targeted drug development with particular emphasis on the genes encoding metabolic enzymes, drug transporters and drug receptors and drug:drug interactions  3. Companion diagnostics and NHS service delivery models  4. Different types and examples of genomic-targeted intervention (examples of genomically-targeted clinical, therapeutic or lifestyle choices) 5. Genomic biomarkers and genetic polymorphisms leading to inter-individual variability in drug response: SNPs, short sequence repeats, haplotypes, DNA epigenetic modifications, e.g. methylation, deletions or insertions, copy number variants, RNA expression levels, RNA splicing, microRNA levels  6. Use of biomarkers and genetic testing in treatments other than cancer </div>  This module aims to provide the student with the in-depth knowledge, understanding and analytical skills to consider the current and emerging research and application of pharmacogenomics and stratified healthcare to ensure a personalised healthcare approach for patients. <div>Objectives  By the end of the course the student should be able to:  1. Discuss and evaluate the mechanism of several examples of genomically-determined  differential drug responses, and adverse drug reactions  2. Appraise the strategies and analytical approaches for stratifying patients for optimal  drug response or to avoid adverse drug reactions; including an awareness of ethnic  differences, and how these translate into the design and utilisation of 'companion  diagnostics 3. Identify and analyse the challenges and limitations of pharmacogenetic  studies  4. Identify and evaluate the different types of current and emerging biomarkers used in personalised medicine  5. Discuss and critically evaluate how genomic information can enable development and utilisation of drug targeted for particular genotypes; including a consideration of pharmacoeconomics  6. Identify the ethical, legal and social issues (ELSI) that could accompany patient stratification for healthcare advice or intervention and discuss the use of patient  stratification to improve the diagnosis and treatment of disease. </div> 1. List the factors influencing the inter-individual variability in patient response to  medication e.g. age, gender, pathology, concomitant medication, lifestyle, adherence  2. Define the terms pharmacogenomics and pharmacogenetics (PGx)  3. Define the terms single nucleotide polymorphism (SNP), haplotype and allelic variant 4. Describe the contribution of large scale Genome Sequencing Projects and genome wide association studies to our understanding of inter-individual pharmacogenetic  variability  5. Describe the impact of PGx on the drug development process  6. Use of PGx in informing clinical trial design  7. Define drug response (efficacy, toxicity and therapeutic window)  8. Describe the pharmaco-economic importance of Adverse Drug Reactions (ADRs) 9. Define adverse drug reaction - how can one be sure it is due to the drug, listing  examples -scoring cases, use of Yellow cards and role of MHRA  10. Understand those aspects of drug response (pharmacokinetics, pharmacodynamics  and immunological hypersensitivity) where pharmacogenetic variability can lead to  ADRs  11. Give examples of metabolic enzymes (especially CYP450s), transporters and receptors which have clinically- significant genetic polymorphisms  12. Know where to find information on inherited variants which affect patient response to  drugs e.g. abacavir-sensitivity, TPMT deficiency, DPD deficiency  13. List examples of specific medications and associated pharmacogenetic tests 14. Briefly, describe the methodology of pharmacogenetic testing  15. List some of the Ethical, Legal and Social Issues (ELSI) surrounding PGx testing 16. List some of the possible patient benefits and limitations (e.g. ethnic variability) of  personalized medicine, time to testing, incomplete relationship  17. List some of the barriers to implementing PGx testing into clinical practice e.g. HCP  education and pharmacoeconomics 18. Describe named examples of drugs, diseases and genes implicated in the areas of  oncology, neuropsychiatry and cardiovascular medicine ? where PGx is either already  influencing practice or likely to influence practice in the near future.  19. Describe what is meant by "Point of care" testing and "Direct to consumer" testing 20. The use of multiplex tests e.g Amplichip, introduction of whole genome sequencing  technologies  21. Describe companion studies and the development of companion diagnostics <ol> <li> Critically evaluate a wide range of information to assist with clinical judgements and decision making.</li> <li> Interpret data and convert into knowledge for use, in a clinical setting, by healthcare colleagues, individual patients and groups of patients</li> </ol> 1. Identify and be able to use appropriate online databases and personalised prescribing tools  2. Know where to find information on pharmacogenetic polymorphisms (SNP, ClinVar,  Ensembl)  3. Know where to find information on genetically-inherited disorders affecting drug  response (OMIM)  4. Know where to find information on pharmacogenetic tests (GTR)  5. Know where to find information on drugs where PGx may be an issue (PharmGKB) 6. Know where to find information on PGx dosing guidelines (CPIC)  7. Work in partnership with NHS colleagues and other professionals (within an  interdisciplinary team) to advise patients and their carers and to optimise patient care. 8. Present information clearly in the form of written reports.  9. Interpret evidence from a range of online resources and integrate this into the sum of  patient information for the interpretation and implementation of pharmacogenetic test  results for patients.  <ol> <li> Actively seek accurate and validated information from a wide range of available sources.</li> <li> Communicate effectively by presenting complex ideas in simple language in both oral and written formats. </li> <li> Self-direct their learning and reflect upon that learning, identifying areas for further improvement.</li> </ol> <div>Prior to teaching  Preliminary reading and self-directed study materials will be sent out to all students  approximately 2 weeks before the course. This is to ensure that prospective students have sufficient familiarity with the scientific background to this study area and to ensure that  they will be able to benefit, fully, from the teaching delivered during the 3 day course.During the 3 day face to face "in house" course  A series of 10 - 15 interactive lectures covering the key themes and concepts. Morning lectures will be followed by group and team-based learning (TBL) activities to  consolidate and further discuss the key content. Afternoons will be hands-on workshops, where students will work individually, in pairs or in small inter-professional groups (IPE). During the workshops they will learn to use, critically  evaluate and apply the knowledge gained in the lectures and group sessions and report  back (verbally) to the rest of the class on their findings.After the course   Assignments will be submitted, via Turnitin, to check for plagiarism, and will be marked  within 3 weeks. Students will receive individualized feedback. E-learning/Blended learning delivered via Blackbaord  Evidence-based learning supported by course notes, reading lists, audio lectures/podcasts, case studies and online tutorials/webinars</div> 1 Written exam 50% 2 Written assignment (inc essay) 50% Personalised verbal and written feedback. MSc Genomic Medicine FT MSc Genomic Medicine FT (HEE) PGDT Taught Component Mandatory MSc Genomic Medicine PT MSc Genomic Medicine PT PGDT Taught Component Mandatory MSc Genomic Medicine PT MSc Genomic Medicine PT (HEE) PGDT Taught Component Mandatory PG Diploma Genomic Medicine FT PG Diploma Genomic Medicine FT PGDT Taught Component Optional PG Diploma Genomic Medicine FT PGDip Genomic Medicine FT(HEE) PGDT Taught Component Optional PG Diploma Genomic Medicine PT PG Diploma Genomic Medicine PT PGDT Taught Component Optional PG Diploma Genomic Medicine PT PGDip Genomic Medicine PT(HEE) PGDT Taught Component Optional PG Cert Genomic Medicine FT PG Cert Genomic Medicine FT PGDT Taught Component Optional PG Cert Genomic Medicine FT PGCert GenomicMedicine FT(HEE) PGDT Taught Component Optional PG Cert Genomic Medicine PT PG Cert Genomic Medicine PT PGDT Taught Component Optional PG Cert Genomic Medicine PT PG Cert Genomic Med PT (HEE) PGDT Taught Component Optional Genomic Medicine - CPD Genomic Medicine - CPD PGDT Taught Component Optional Genomic Medicine - CPD Genomic Medicine - CPD (HEE) PGDT Taught Component Optional Y New Clinical Genetics, Second Edition, by Andrew Read and Dian Donnai Rang & Dale's Pharmacology 8th Edition  Authors: James Ritter Rod Flower Graeme Henderson Humphrey Rang Attia J, Ioannidis JP, Thakkinstian A, McEvoy M, Scott RJ, Minelli C, Thompson J, Infante Rivard C, Guyatt G. How to use an article about genetic association: A: Background  concepts. JAMA. 2009 Jan 7;301(1):74-81. doi: 10.1001/jama.2008.901. Erratum in:  JAMA. 2009 Mar 11;301(10):1024  Relling MV, Evans WE. Pharmacogenomics in the clinic. Nature. 2015 Oct 15;526(7573): 343-50. doi: 10.1038/nature15817. PMID: 26469045  Collins SL, Carr DF, Pirmohamed M. Advances in the Pharmacogenomics of Adverse  Drug Reactions. Drug Saf. 2016 Jan;39(1):15-27.PMID: 26650062  Sim SC, Kacevska M, Ingelman-Sundberg M. Pharmacogenomics of drug-metabolizing  enzymes: a recent update on clinical implications and endogenous effects.  Pharmacogenomics J. 2013 Feb;13(1):1-11. PMID: 23089672  Yiannakopoulou ECh. Pharmacogenomics of phase II metabolizing enzymes and drug  transporters: clinical implications. Pharmacogenomics J. 2013 Apr;13(2):105-9. PMID:  23044602 0 0 150