1. Pharmacogenetics The Impact of Genomics on Public Health Cardiff, 6 th November 2014 Ana Alfirevic The Wolfson Centre for Personalised Medicine Department of Molecular and Clinical Pharmacology University of Liverpool

2. Pharmacogenetics/pharmacogenomics the study of how genetic differences among individuals cause various responses to a drug in terms of both, efficacy and safety Pharmacogenetics/pharmacogenomics the study of how genetic differences among individuals cause various responses to a drug in terms of both, efficacy and safety

3. Pharmacogenetic testing Drug efficacy “The vast majority of drugs - more than 90 per cent – only work in 30 or 50 per cent of the people” (GSK) Drug safety Adverse drug reactions are common-6.5% hospital admissions in the UK (Pirmohamed 2004), ADRs vary in severity Drug Dosing Drugs with narrow therapeutic index

4. Personalised Medicine Stratified Medicine Precision Medicine

5. BBC News

6. Direct to Consumer Genotyping Services PERSONAL GENOME

7. DNA collection kit

8. Health Inequalities Is this going to be reserved only for the reach within society? Will it only be used in high income countries? Is it going to exacerbate health inequalities?

9. FDA- Pharmacogenomic Biomarkers in Drug Labelling Drug labelling may contain information on genomic biomarkers and can describe: – Drug exposure and clinical response variability – Risk for adverse events – Genotype-specific dosing – Mechanisms of drug action – Polymorphic drug target and disposition genes FDA-approved drugs with pharmacogenomic information in their labelling N=144

10. Drug safety

11. Dear Dr Alfirevic, 29 year old Epilepsy Treatment with antiepileptic drug carbamazepine (CBZ) Good seizure control, however... 6 weeks after starting therapy SKIN RASH, jaundice I read your article –biomarker HLA- A*31:01 associated with CBZ-induced skin rash My PERSONAL GENOME contains several risk alleles HLA alleleSNPMy genotype HLA-B*1502Rs3909184GG HLA-B*1502rs2844682GG HLA-B*1502rs9271366AA HLA-B*1502rs3130690GG HLA-B*1502rs1058026AA HLA-B*5801rs3117583AG HLA-B*5801rs1058026AA HLA-B*5701rs2395029TT HLA-B*5701rs3093726TT HLA-A*3101rs1633021 CT HLA-A*3101rs1061235AA HLA-A*3101rs2571375AA HLA-A*3101rs1116221CT HLA-A*3101rs2844796AG HLA-A*3101rs1736971GT HLA-A*3101rs1611133CT HLA-A*3101rs2074475TT HLA-A*3101rs7760172TT HLA-A*3101rs2517673GG HLA-A*3101rs12665039TT HLA-A*3101rs1362088TT

12. Dear Dr Alfirevic, 29 year old Epilepsy Treatment with antiepileptic drug carbamazepine (CBZ) Good seizure control, however... 6 weeks after starting therapy SKIN RASH, jaundice I read your article –biomarker HLA- A*31:01 associated with CBZ-induced skin rash My PERSONAL GENOME contains several risk alleles HLA alleleSNPMy genotype HLA-B*1502Rs3909184GG HLA-B*1502rs2844682GG HLA-B*1502rs9271366AA HLA-B*1502rs3130690GG HLA-B*1502rs1058026AA HLA-B*5801rs3117583AG HLA-B*5801rs1058026AA HLA-B*5701rs2395029TT HLA-B*5701rs3093726TT HLA-A*3101rs1633021 CT HLA-A*3101rs1061235AA HLA-A*3101rs2571375AA HLA-A*3101rs1116221CT HLA-A*3101rs2844796AG HLA-A*3101rs1736971GT HLA-A*3101rs1611133CT HLA-A*3101rs2074475TT HLA-A*3101rs7760172TT HLA-A*3101rs2517673GG HLA-A*3101rs12665039TT HLA-A*3101rs1362088TT What is my genetic risk for SKIN RASH with antiepileptic drugs ?

13. Immune mediated ADRs Rare, but could be life threatening (30% fatality) 1 in 1,000 to 1 in 10,000 patients on antiepileptic drug CBZ develop severe skin reactions Drug-induced exanthema Toxic Epidermal Necrolysis

14. Immune-mediated ADRs- drug hypersensitivity Caused by diverse classes of drugs Antiepileptics Antiretrovirals (anti HIV) Antimicrobials Anti gout Non-steroidal anti-inflammatory Caused by diverse classes of drugs Antiepileptics Antiretrovirals (anti HIV) Antimicrobials Anti gout Non-steroidal anti-inflammatory

15. Diagnosis Clinical Absence of safe, validated diagnostic test to confirm the diagnosis Phenotype Standardisation Project (Pirmohamed et al., 2011) In vivo tests Skin patch test (specificity, sensitivity unknown) Re-challenge In vitro research tools Lymphocyte toxicity assay (LTA) Lymphocyte transformation test (LTT)

16. Human leukocyte antigen (HLA) associations with hypersensitivity reactions

17. HLA alleles Class I Class III Class II Class I Class III Class II TNF LTA HSP-70 Chromosome 6 The most polymorphic region in human genome Immune function HLA complex helps the immune system distinguish the body's own proteins from proteins made by foreign invaders such as viruses and bacteria

18. Clinical utility of genetic testing Abacavir Hypersensitivity Phenotype Association with HLA-B*57:01 Genotype antiretroviral drug 9% hypersensitivity immunogenetic etiology

19. Clinical utility of genetic testing Abacavir Hypersensitivity Phenotype Association with HLA-B*57:01 Genotype antiretroviral drug 9% hypersensitivity immunogenetic etiology Pre-treatment genetic testing → Reduced hypersensitivity (Mallal, NEJM, 2008) Pre-treatment genetic testing → Reduced hypersensitivity (Mallal, NEJM, 2008)

20. ITCH - International Consortium on Drug Hypersensitivity Liverpool- global co- ordinating centre for ITCH study for the International Serious Adverse Event Consortium (iSAEC) Aim- to recruit patients with hypersensitivity reactions to a variety of drugs 1,500 patients with most severe skin ADRs

21. Antiepileptic drug-induced hypersensitivity reactions DrugPhenotype SJS/TEN Phenotype DRESS Phenotype MPE Population CarbamazepineHLA- B*15:02 HLA- A*31:01 Asian CarbamazepineHLA- A*31:01 Caucasian LamotrigineHLA- B*15:02 Asian PhenytoinHLA- B*15:02 CYP2C cluster Asian

22. Carbamazepine-induced SJS/TEN and HLA- B*1502 in Asian populations HLA-B*1502 testing → 0 incidence of SJS/TEN

23. Meta-analysis of HLA-A*31:01 and CBZ-hypersensitivity Yip et al, 2012 ALL PHENOTYPES, DIFFERENT ETHNICITIES

24. Panel of HLA markers 22 HLA markers are associated with drug-induced toxicity Developing assays to determine all these markers in individuals before prescribing a number of drugs Low cost tests Short time-to-results Low volume of whole blood

25. Portable genotyping device Battery powered Real-time results without need for PC connectivity Isothermal amplification

26. Dear Dr Alfirevic, 29 year old Epilepsy Treatment with antiepileptic drug carbamazepine (CBZ) Good seizure control, however... 6 weeks after starting therapy SKIN RASH, jaundice I read your article –biomarker HLA- A*31:01 associated with CBZ-induced skin rash My PERSONAL GENOME contains several risk alleles HLA alleleSNPMy genotype HLA-B*1502Rs3909184GG HLA-B*1502rs2844682GG HLA-B*1502rs9271366AA HLA-B*1502rs3130690GG HLA-B*1502rs1058026AA HLA-B*5801rs3117583AG HLA-B*5801rs1058026AA HLA-B*5701rs2395029TT HLA-B*5701rs3093726TT HLA-A*3101rs1633021 CT HLA-A*3101rs1061235AA HLA-A*3101rs2571375AA HLA-A*3101rs1116221CT HLA-A*3101rs2844796AG HLA-A*3101rs1736971GT HLA-A*3101rs1611133CT HLA-A*3101rs2074475TT HLA-A*3101rs7760172TT HLA-A*3101rs2517673GG HLA-A*3101rs12665039TT HLA-A*3101rs1362088TT What is my genetic risk for SKIN RASH with antiepileptic drugs ? NO RISK ALLELES FOR CARBAMAZEPINE

27. NATURE GENETICS, 26 th October 2014 2-5% children <5y febrile seizures Febrile seizures following measles, mumps and rubella vaccination 3x risk  interferon-stimulated gene IFI44L, P=5.9 x 10 -12 measles virus receptor CD46, P=9.6 x 10 -11

28. Interferon-stimulated gene (IFI44L)

29. Efficacy/Drug dosing

30. Number of users UK:600,000 Dose (mg) range per day:0.5-20 Fold variability in dose:40 Major bleeding rate per 100-person years: 2.6 2.6 Ranking in ADR list: 3 Warfarin Approved for human use in 1954

32. VKORC1 Carboxylase epoxidase Warfarin R CYP1A2 CYP3A4 Metabolites Warfarin S CYP2C9 Vitamin K Clotting factors II, VII, IX, X

33. GWAS Warfarin Mean Weekly Dose (UK Prospective Cohort; n=714) CYP2C9 VKORC1

34. Determinants of Anticoagulation Control McLeod and Jonas, 2009

35. European Pharmacogenetics of Anticoagulation Therapy (EU-PACT) Trial Randomise Loading dose calculation Dose adjustment Intervention Arm (Genotype guided) Control Arm (Non-genotype guided) 3 month follow up Outcome comparison Loading dose calculation Dose adjustment

36. Pharmacogenetic-Based Dosing: Warfarin Randomised Controlled Trial FP7 sponsored EU trials 454 patients 226 in genotype arm 228 in standard care arm Point of Care test for genotyping European Union Pharmacogenetics of AntiCoagulant Therapy

37. Genotyped arm %TTR Standard dosing (control) arm %TTR Adjusted Difference P value ITT ANALYSIS (n= 211 vs 216) 67.4%60.3%7%P<0.001 PER-PROTOCOL (n=166 vs 184) 68.9%62.3%6.6%P=0.001 PRIMARY OUTCOME MEASURE: Percent time within therapeutic INR range 2.0- 3.0 (TTR) during 12 weeks following the initiation of warfarin therapy

38. Differences Between Genotyped- Guided Group and Control Group Time in Therapeutic RangeInternational Normalized Ratio

39. No difference between genotyped and control arm US COAG investigators Kimmel SE et al. N Engl J Med 2013;369:2283-2293.

40. Nov 23, 2013

41. Differences between EU-PACT and COAG warfarin studies Patient heterogeneity greater in COAG Genotyping not available in ~50% of patients prior to first dose in COAG Did not utilise CYP2C9 polymorphisms on day 1

42. Dosing Algorithms EU-PACT Day 1-3: Loading dose algorithm Day 4/5: Dose revision algorithm Up to 3 months: AC clinics (computerised dosing) COAG Day 1-3: Maintenance dose algorithm Day 4/5: Dose revision algorithm Up to 1 month: Protocol driven S-warfarin elimination half-life: 18-35 hours Time to steady state: 90-175 hours Dose revision algorithm on day 4 dependent on INR What proportion of patients will have had a change in INR by day 4? S-warfarin elimination half-life: 18-35 hours Time to steady state: 90-175 hours Dose revision algorithm on day 4 dependent on INR What proportion of patients will have had a change in INR by day 4?

43. Conclusions New technologies to investigate genetic factors in drug response Strong genetic associations related to drug safety and efficacy Slow clinical implementation of genetic tests Patient and general public requests for interpretation of genetic tests Further functional work and next-gen sequencing to define causal variants associated with drug efficacy and toxicity