1. Pharmacogenetics and Pharmacogenomics Eric Jorgenson 2/24/9

2. Outline Introduction Introduction Examples Examples Pharmacogenetics Pharmacogenetics Pharmacogenomics Pharmacogenomics Environment and Drug Response Environment and Drug Response Additional Resources Additional Resources

3. What is Pharmacogenetics? The study of the role of inheritance in the individual variation in drug response. The study of the role of inheritance in the individual variation in drug response. How it differs from disease genetics How it differs from disease genetics Gene-environment interaction Gene-environment interaction Can involve multiple gene-environment interactions Can involve multiple gene-environment interactions Ethical/Methodological constraints Ethical/Methodological constraints

4. Events in Pharmacogenetics Meyer Nature Reviews Genetics 2004

5. PTC and Pharmacogenetics Meyer Nature Reviews Genetics 2004

6. Bimodal Distribution of PTC Non-RespondersRespondersNo ToxicityToxicity

7. Diplotype and PTC Score Kim et al. Science 2003

8. Adapted from Bufe et al. Current Biology 2005

9. Pharmacogenetic Study Design Family Studies Family Studies Linkage Analysis Linkage Analysis Family and Linkage are difficult to do for some phenotypes: Family and Linkage are difficult to do for some phenotypes: Severe toxicity Severe toxicity Rare diseases (need multiple affected family members) Rare diseases (need multiple affected family members)

10. Pharmacogenetic Study Design: Candidate Gene Studies Phenotype-to-Genotype Phenotype-to-Genotype Identify a drug response phenotype Identify a drug response phenotype Choose a candidate gene Choose a candidate gene Genotype-to-Phenotype Genotype-to-Phenotype Identify genetic polymorphisms in a gene of interest Identify genetic polymorphisms in a gene of interest Choose study subjects with different genotypes Choose study subjects with different genotypes Give probe drug to subjects Give probe drug to subjects Smaller sample size needed Smaller sample size needed Best for measuring pharmacokinetic response Best for measuring pharmacokinetic response

11. Drug transport, targeting, and metabolism

12. Pharmacodynamics What a drug does to the body What a drug does to the body Usually refers to the interaction of the drug with the drug target Usually refers to the interaction of the drug with the drug target Pharmacogentics: Polymorphisms in the drug target Pharmacogentics: Polymorphisms in the drug target

13. Pharmacokinetics How a drug is processed by the body How a drug is processed by the body ADME ADME Absorption Absorption Distribution Distribution Metabolism Metabolism Excretion Excretion Drug Levels Drug Levels Efficacy Efficacy Toxicity Toxicity

14. Drug levels in the body Plasma concentration Plasma concentration Therapeutic window Therapeutic window Metabolic Ratio Metabolic Ratio Compare blood vs. urine Compare blood vs. urine Probe drug Probe drug Can be measured over time Can be measured over time

15. Outline Introduction Introduction Examples Examples Pharmacogenetics Pharmacogenetics Pharmacogenomics Pharmacogenomics Environment and Drug Response Environment and Drug Response Additional Resources Additional Resources

16. Phillips et al. JAMA 2001

17. Thiopurine S-methyltransferase (TPMT) Drugs: Drugs: 6-mercaptopurine 6-mercaptopurine azathiopurine azathiopurine Diseases: Diseases: Acute lymphoblastic leukemia Acute lymphoblastic leukemia Inflammatory bowel disease Inflammatory bowel disease Toxicity: Toxicity: Fatal myelosuppression Fatal myelosuppression Hematopoietic toxicity Hematopoietic toxicity

18. TPMT and 6-mercaptopurine

19. Pharmacogenetics of TPMT

20. TPMT Haplotypes and Activity

21. Standard TPMT Dosing

22. Drug Exposure and Toxicity

23. Genotype Specific TPMT Dosing

24. Drug Exposure and Toxicity

25. Pharmacogenetics of Acetylation Weinshilboum NEJM 2003

26. NAT2 and Race/Ethnicity

27. Pharmacogenetics of CYP2D6 Weinshilboum NEJM 2003

28. CYP2D6 Copy Number Polymorphism and Nortriptyline Metabolic Ratio Meyer Nature Reviews Genetics 2004

29. Plasma Concentration of Nortriptyline vs. CYP2D6 Copy Number Weinshilboum NEJM 2003

30. CYP2D6 and Race/Ethnicity

31. Pharmacogenetics and Race/Ethnicity Weinshilboum NEJM 2003

32. Drug Metabolism and ADRs

33. Outline Introduction Introduction Examples Examples Pharmacogenetics Pharmacogenetics Pharmacogenomics Pharmacogenomics Environment and Drug Response Environment and Drug Response Additional Resources Additional Resources

34. Pharmacogenetics and Pharmacogenomics

35. What is Pharmacogenomics and how is it different from Pharmacogenetics? Genomic scale Genomic scale Array based platforms Array based platforms DNA: genetic variation DNA: genetic variation RNA: gene expression RNA: gene expression Protein: protein activity Protein: protein activity

36. Pharmacogenomics Evans and Relling Nature 2004

37. Genome-wide Association and Drug Response GWAS Catalog: http://www.genome.gov/26525384 GWAS Catalog: http://www.genome.gov/26525384 http://www.genome.gov/26525384 Nicotine Dependence Nicotine Dependence Long QT Syndrome Long QT Syndrome Statin-induced Myopathy Statin-induced Myopathy

38. Study of the Effectiveness of Additional Reductions in Cholesterol and Homocysteine (SEARCH) Randomized Trial Randomized Trial 12,064 participants 12,064 participants Prior MI Prior MI Simvastatin: 80mg vs. 20mg Simvastatin: 80mg vs. 20mg 6,031 on 80mg 6,031 on 80mg 49 definite myopathy cases 49 definite myopathy cases 49 incipient myopathy cases 49 incipient myopathy cases SEARCH Consortium NEJM 2008

39. Selection of subjects for genotyping 96 cases on 80mg simvastatin 96 cases on 80mg simvastatin 48 definite myopathy 48 definite myopathy 48 incipient myopathy 48 incipient myopathy 96 matched controls on 80mg simvastatin 96 matched controls on 80mg simvastatin Sex Sex Age Age eGFR eGFR Amiodarone use Amiodarone use SEARCH Consortium NEJM 2008

40. Subjects and Genotyping platform 85 cases, 90 controls 85 cases, 90 controls 1 case dropped for non-European ancestry 1 case dropped for non-European ancestry Others dropped for lack of DNA Others dropped for lack of DNA Illumina HumanHap300 Illumina HumanHap300 318,237 SNPs 318,237 SNPs 316,184 SNPs passed QC 316,184 SNPs passed QC SEARCH Consortium NEJM 2008

41. Manhattan Plot of GWAS SEARCH Consortium NEJM 2008

42. Replication (?) Heart Protection Study Heart Protection Study 40mg simvastatin vs. placebo 40mg simvastatin vs. placebo 40mg: 23 myopathy cases 40mg: 23 myopathy cases Placebo: 9 myopathy cases Placebo: 9 myopathy cases 16,664 genotyped participants 16,664 genotyped participants 21 cases 21 cases 16,643 controls 16,643 controls Relative Risk = 2.6 per allele Relative Risk = 2.6 per allele Compared to Odds Ratio = 4.4 per allele Compared to Odds Ratio = 4.4 per allele SEARCH Consortium NEJM 2008

43. Myopathy attributable to rs4149056 within patients on 80mg of Simvastatin SEARCH Consortium NEJM 2008

44. Gene Expression Diagnostic Test Oncotype DX Oncotype DX Oncotype DX Oncotype DX Tests expression of 21 genes in tumor samples Tests expression of 21 genes in tumor samples Recurrence Score of 0-100 Recurrence Score of 0-100 Women with higher scores are more likely to benefit from chemotherapy Women with higher scores are more likely to benefit from chemotherapy

45. Outline Introduction Introduction Examples Examples Pharmacogenetics Pharmacogenetics Pharmacogenomics Pharmacogenomics Environment and Drug Response Environment and Drug Response Additional Resources Additional Resources

46. Pharmacoenvironment Grapefruit juice-felodipine interaction Grapefruit juice-felodipine interaction bergamottin inhibition of CYP3A4 in the small intestine bergamottin inhibition of CYP3A4 in the small intestine

47. Drug levels Dahan and Altman EJCN 2004

48. Grapefruit juice drug interactions Dahan and Altman EJCN 2004

49. Outline Introduction Introduction Examples Examples Pharmacogenetics Pharmacogenetics Pharmacogenomics Pharmacogenomics Environment and Drug Response Environment and Drug Response Additional Resources Additional Resources

50. Reviews of Pharmacogenetics Evans and Mcleod NEJM 2003 Evans and Mcleod NEJM 2003 Goldstein, Tate, Sisodiya Nature Reviews Genetics 2003 Goldstein, Tate, Sisodiya Nature Reviews Genetics 2003 Meyer Nature Reviews Genetics 2004 Meyer Nature Reviews Genetics 2004 Evans and Relling Nature 2004 Evans and Relling Nature 2004 Wilkinson NEJM 2005 Wilkinson NEJM 2005

51. More on Pharmacogenetics Pharmacogenetics Knowledge Base (PharmGKB) Pharmacogenetics Knowledge Base (PharmGKB)PharmGKB http://www.PharmGKb.org http://www.PharmGKb.org

52. More Examples Evans and Mcleod NEJM 2003

53. Even more Examples Evans and Mcleod NEJM 2003