1. Common variants vs Rare variants

2. The 1000 genome project consortium, Nature 2012

3. The 1000 genome project consortium, Nature 2012

4. Pharmacogenetic variants
Genetic variants often differ according to ancestry, which can confound the translation of pharmacogenetic traits from one population to another
Pharmacogenetic variants
- CYP2C9*8 and CYP2C9*11 found in 5% of African Americans but rare in Caucasians
- CYP2C rs also influenced warfarin pharmacogenetics in African-American independently of CYP2C9*2 and CYP2C9*3
Pirmohamed et al., Trend Pharm Sci 2015

5. NUDT15 variants and bone marrow suppression during treatment with thiopurines
NUDT15 is an enzyme with pyrophosphatase activity, capable of removing oxidatively damaged forms of guanine from nucleotide pools, preventing their incorporation in nucleic acids.
rs is a variant frequent in Asian patients rare in Caucasian patients.

6. NUDT15 variants are associated with mercaptopurine dose requirements in children with leukemia
Yang et al., J Clin Oncol 2015

7. Effetti delle varianti genetiche sui fenotipi (anche farmacogenomici)
Dipendono da:
- tipo di variante: SNP? indel? CNA?
- posizione nel genoma: esonico? intronico? regione regolatrice? intergenico?
- effetto sulla sequenza: sinonimo/non sinonimo?
- frequenza della variante: rara? frequente? varianti più frequenti in genere hanno effetti più deboli sul fenotipo rispetto alle varianti più rare
modello di ereditarietà: omozigosi/eterozigosi? effetto dominante/recessivo/co-dominante?
linkage: diretto? da linkage disequilibrium?
monogenico/poligenico?

8. Which SNPs are important? SNP = Single Nucleotide Polymorphism
A …G A G C A C A T …..
B …G A T C A C A T …..
Which SNPs are important?
DNA sequence
A …G A G C A C A T …..
B …G A T C A C A T …..
Protein codified
Functional
Non-functional
SNP = Single Nucleotide Polymorphism

9. Effetto del polimorfismo genetico sull’attività della proteina (1)
Pt 1
Pt 2
Pt 3
= allele funzionale (wild type )
= gene non-funzionale (variante con SNP, I/D, ecc)
Evans et al, SJCRH, 2000

10. Effetto del polimorfismo genetico sull’attività della proteina (2)
Evans et al, SJCRH, 2000

11. Ereditarietà: codominanza
Goodman and Gilman, 2011

12. Haplotypes of UGT1A1 gene generated by Haploview
Goodman and Gilman, 2011

13. Antipirin half-life in twins
Vessel & Page, Science 1968
Goodman and Gilman, 2011

14. (Dolan et al Cancer Res 2004; Watters et al PNAS 2004)
Cancer Phenotypes are determined in Cell lines, and HapMap genotypes can be used for genome-wide phenotype/genotype association studies
~ 30% - 70% of pharmacodynamic variability (how drugs affect humans) is genetic
(Dolan et al Cancer Res 2004; Watters et al PNAS 2004)

15. Fenotipi farmacologici di tipo farmacocinetico hanno una componente genetica di fenotipi più complessi (clinici) +
- Half-life
- Steady-state concentration
Pharmacokinetic
Variability explained by genetics
Drug response phenotypes
- In vitro drug senstivitity
Pharmacodynamic
- Drug response
- Drug-induced adverse effects
Clinico -

16. Personalized medicine should help clinicians in:
Personalized medicine for pediatric inflammatory bowel disease The aim of personalized medicine is to provide the most appropriate cure to the right patient, at the right dose and at the right time
Personalized medicine should help clinicians in:
- Indentifying patients who will not respond to therapies
- Finding patients at risk of adverse effects
- Choosing ideal drug, dose, and employing less expensive agents.

17. Pharmacological tools for personalized medicine
DNA genetic polymorphisms
Gene expression signatures
Epigenetic markers (e.g DNA methylation, microRNA)
Genomic Biomarkers
Drug metabolites concentrations
Drug clearance
Activity of enzymes involved in drug metabolism
Pharmacokinetic assays
Patient’s cell sensitivity to drugs evaluated in vitro
Pharmacodynamic assays
Stocco et al., Current Pharmaceutical Design, 2012

18. Biotransformation of thiopurines
Stocco et al. J Clin Gastroenterol 2013

19. TPMT activity is inherited as an autosomal codominant trait
Caucasian population
Weinshilbaum and Sladek, Am J Hum Genet 1980

20. Example of genomic marker for personalized medicine: tiopurine-S-methyl-transferase (TPMT)
Enzyme of phase-II drug metabolism that catalyzes the methylation of thiopurines (6-mercaptopurine, 6-thioguanine) and other aromatic thiols.

21. Tiopurine-S-methyl-transferase (TPMT)
Physiologically, TPMT is involved in the biosynthesis of a cofactor that confers molibdenum binding propreties to proteins.
MDO meeting, Stuttgart 2014

22. How to study TPMT gene variants?
Genotyping three SNPs allows to identify 95% of patients with reduced TPMT activity in Caucasians.
TPMT*2
TPMT*3

23. Official database of TPMT variant alleles

24. The protein encoded by the TPMT
The protein encoded by the TPMT*3A variant allele is less stable than that encoded by the TPMT*1 (wild-type) allele
Dr. Evans’s lab (Tai et al., PNAS 1997)
picture from Jones TS et al, Clin Pharm Ther 2007

25. Cheok & Evans, 2006

26. Cheok & Evans, 2006

28. not
Relling et al., CPT 2013

29. MERCAPTOPURINE and TPMT
GUIDELINES are designed to help clinicians by
recommending the best pharmacogenetic test to perform
Interpreting the pharmacogentic test results
to optimize drug therapy

30. MERCAPTOPURINE and TPMT