Farmacogenetica
Prof. dr. Henk-Jan Guchelaar
Klinische Farmacie & Toxicologie
Leids Universitair Medisch Centrum
Leiden Academic Center for Drug Research
COIG – Genoom en Genetica
30 NOVEMBER 2018
Farmacogenetica-paspoort
Three patients at the outpatient clinic
Three patients A, B, C
Identical:
• Symptoms
• Diagnostic procedures
• Diagnosis X
• Treatment: Drug Rx at a dose x mg/day
Three patients at the outpatient clinic
e x mg/day
After 3 weeks
• Pat A: still symptoms, no effect of drug
• Pat B: symptoms resolved
• Pat C: still symptoms, side effects
How is this possible?
‘Most drugs don’t work’
Effective (%)…..
Alzheimer 30
Depression (SSRI) 62
Asthma 60
Diabetes mellitus 57
Incontinence 40
Migraine (acute) 52
Migraine (profyl.) 50
Cardiac dysrhythmia 60
Tumors 25
Schizophrenia 60
Rheumatoid arthritis 50
Reumat. art. (Cox-2) 80
Hepatitis C 47
Spear, Trends Mol Med 2001;7(5):201
Prescribing drugs – Trial and Error
Dx Guideline
Rx Clinical studies
•Dx
•Inclusion criteria
•Age
•Organ function
•Severity of disease
First choice Drug
•‘Normal’ dose
•Individualize
•Co-morbidity
•Co-medication
•Age, Organ function
Monitor effect
•Efficacy & Toxicity
•Tumorsize, Biomarkers
•Pain(score), Bloodpressure
•Cholesterol levels
•Liverfunction, Myalgia
Drug dose
•Increase/decrease
Switch drug
•Second choice Drug
Variability in humans
Drug response is a heritable trait
9
Mei 1975: Debrisoquine
Debrisoquine – 4-hydroxydebrisoquine
Smith, Lancet 1977(2): 584-586
Pharmacogenetics in drug labels
132 drug labels contain PGx information
Farmacogenetische informatie in drug labels
www.pharmgkb.org
14
November 2018: CYP2D6 genotypering
Van genotype naar fenotype
Roche, AmpliChip CYP450 Test, manual
P
Allel Enzym
activiteit
Genetische variant Allel frequentie (%)
Kaukasiers (Europa) Japan Tanzania
*1 Normaal Wild-type 32.2-36.4 43 27.8
*2 Normaal 2850C>T, 4180G>C 28.5-32.4 12.3 40
*2x2 Hoog duplicatie 1-1.3
*3 Afwezig 2549delA 1-2 0
*4 Afwezig 1846G>A 17.2-20.7 .2 .9
*5 Afwezig CYP2D6 deletie 2-6.9 4.5 6.3
*6 Afwezig 1707delT .9-1.3 0
*9 Gereduceerd 2615_2617delAAG 1.8-2.7
*10 Gereduceerd 100C>T 1.5-2 38.1 3.8
*17 Gereduceerd 1023C>T, 2850C>T 17
*41 Gereduceerd 2988G>A 8.4
CYP2D6 genotype
Fenotype : Poor Metabolizer (5-10%)
Intermediate Metabolizer (10-15%)
Single Nucleotide Polymorfisme
“Book of Life”
Complete sequentie humane genoom
bekend
“voor iedereen gelijk”
Typografische fouten:
Letter mis.
Letter teveeel
Verwissleing
Typefouc
Dupliplipliplicatiesssss
Hele paragrafen dubbeldubbel
Passages missen
Dreekegmo
Check, Nature 2005:1084
Variabiliteit in DNA
2 niet verwante individuen:
3.200 * 106 baseparen
1: 300-1000 baseparen zijn
verschillend
3-10 * 106 baseparen zijn
verschillend
99,7-99,9% overeenkomst
Kleine verandering … grote gevolgen
Courtesy: GJ van Ommen, sept 2012
DEZE ZIN IS HEEL GOED TE LEZEN
DEZE ZIN IS GOED TE LEZEN
DEZE ZNI SH EELG OE DTELE ZEN
I
21
Variaties in het DNA
Deleties
• DNA
• Eiwit
SNPs
• DNA
• Eiwit
Microsatellieten
Wild type Mutant
GAA AAG CCT GGT GAA GCC TGG TGA
Glu Lys Pro Gly Glu Ala Trp Stop
ATG AAC CCG ATG AAC TGG
Met Asn Arg Met Asn Trp
ATGAATATATATATATAGGC
Niet alleen lever-enzymen
Compliance
Absorptie
Metabolisme
Eliminatie
Target/Receptor
Signaal transductie
Farmacogenetica
100% Dose
Drug A
50% Dose
Drug A Drug B
DNA Test
Hoe vaak komt het voor?
A: zeldzaam (1-2%)
B: vrij zeldzaam (2-5%)
C: redelijk vaak (25-50%)
D: Bijna iedereen heeft wel een ‘actionable’ variant
0%
20%
40%
60%
80%
100%
PGx-panel approach
‘Actionable’ genotypes
Dunnenberger, Annu Rev Pharmacol Toxicol 2015
95% of patients have at least 1 ‘actionable’’ genotype
Evidence supporting a panel approach:
Brixner, J Med Econ, 213-228. 2016
Finkelstein, PGx and Pers Med 2016:9 107–116
Elliot, PLoS One. 2017 Feb 2;12(2): e0170905
Dutch Pharmacogenetics Working Group
27 Swen, Clin Pharmacol Ther 2008;83(5):781-8
12 members multidisciplinary (DPWG): (clinical) pharmacists, physicians, clinical pharmacologists, clinical
chemists, epidemiologist, toxicologist, primary care physician
Aim: • To develop pharmacogenetic (dosing)guidelines based
upon systematic review of literature
• To integrate these guidelines in electronic prescription
systems and medication surveillance systems
2018: guidelines for 94 gene-drug pairs
47 actionable
interactions
• Top 50 lijst gen-geneesmiddel
combinaties
• Systematisch literatuur onderzoek
~1000 artikelen
• Scoren ‘level of evidence’
• Scoren ‘klinische relevantie’
• Status rapport
• Gen-geneesmiddelinteractie: ja/nee
• Actie vereist: ja/nee
• Evidence based therapeutische
richtlijn
Farmacogenetica werkgroep - werkwijze
Swen, Clin Pharmacol Ther 2008;83(5):781-8
PGx: improving efficacy or preventing toxcity?
Bank, Clin Pharmacol Ther. 2017;103(4):599-618
Preventing toxicity Improving efficacy
CYP2C9 phenytoin; warfarin; acenocoumarol, phenprocoumon
CYP2C19 (es)citalopram; imipramine; sertraline; voriconazole
CYP2C19 clopidogrel; voriconazole; lansoprazole, omeprazole, pantoprazole
CYP2D6 amitriptyline; clomipramine; codeine (CI); doxepine; imipramine; nortriptyline, aripiprazole
CYP2D6 amitriptyline; clomipramine; codeine; doxepine; imipramine; nortriptyline; paroxetine, atomoxetine
CYP3A5 CYP3A5 tacrolimus
DPYD capecitabine; fluorouracil; tegafur
HLA-B abacavir; carbamazepine, allopurinol, phenytoin, flucloxacillin
SLCO1B1 simvastatin,atorvastatin
TMPT azathioprine; mercaptopurine; thioguanine
VKORC1 warfarin, acenocoumarol, phenprocoumon
UGT1A1 irinotecan
CYP2B6 efavirenz
Actionable interactions
RCTs in Pharmacogenetics
Drug Clinical Endpoint Variant
Abacavir hypersensitivity HLA-B*5701
Acenocoumarol / Fenprocoumon
% time between therapeutic INR
VKORC1/CYP2C9
Warfarin % time between therapeutic INR
VKORC1/CYP2C9
Warfarin % time between therapeutic INR
VKORC1/CYP2C9
Mercaptopurine leucopenia TPMT
Warfarin major bleeding, INR>4, venous thromboembolism
VKORC1/CYP2C9/CYP4F2
Abacavir – HLA-B *5701
33
Abacavir – HLA-B *5701
Hypersensitivity
• 5-8% Caucasians
• Rechallenge can be fatal
HLA-B *5701
Rodriguez, Pharmacogenomics 2008;9(10): 1531
Abacavir overgevoeligheid
• 1,956 patiënten
• 1:1 gerandomiseerd : screening vs no screening
• Prevalentie HLA-B *5701= 5,6% (109 patiënten)
• “Our results show that a PGx test can be used to prevent a specific toxic effect of a drug”
Mallal, N Engl J Med 2008;358(6):568
NPV= 100%; PVV= 48%
SPC “Voor het starten van de behandeling met abacavir zou elke hiv-patiënt gescreend moeten worden op
het drager zijn van het HLA-B*5701-allel, ongeacht het ras (zie rubriek 4.4). Abacavir moet niet worden
gebruikt bij patiënten die drager zijn van het HLA-B*5701-allel.
35
Abacavir – HLA-B *5701
Caucasian 4.2-7.6%
• South Europe 1-4
• Mediterranen 1-2
Asian
• USA 1
• China 0
• Japan 0
• Thailand 4-10
• India 5-20
• Middle East 1-2
African 0.2-3
African-American 2.4-9.0
Hispanics 1.9-4.7
Indians 2.1
Azathioprine/mercaptopurine metabolisme
AZA
Actieve stof Thioguanine nucleotide
6-MP
TPMT
Afbraak producten
Beenmerg-suppressie
Intervention Control RR (95%CI)
Total (n) 399 370
Hematological side effect 29 (7,2%) 29 (7,8%)
TPMT variant 1 / 39 (2,6%) 8 / 35 (22,9%) 0,11 (0,01-0,85)
No TPMT variant 29 / 360 (8,1%) 22 / 335 (6,6%) 1,2 (0,72-2,09)
• 783 IBD patients; mercaptopurine or azathioprine
• 1:1 randomized to screening vs no screening TPMT*2, TPMT*3A, and TPMT*3C
• HET: 50% dose reduction, HOM 90% dose reduction
• Primairy endpoint: leuko’s < 3.0*10(9)/L or platelets < 100*10(9)/L)
• “10-fold reduction in hematologic ADRs among variant carriers without differences in
treatment efficacy”
Coenen MJ, Gastroenterology. 2015 907-17
Thiopurine response Optimization by Pharmacogenetic testing
in Inflammatory bowel disease Clinics
TOPIC TRIAL
Number needed to genotype
• How many patients do I have
to screen/test to prevent one
from having a Adverse Drug
Reaction (grade 3-4 toxicity,
death, etc.)?
NNG for TPMT testing in Topic
• Hematological ADR: leuko’s < 3.0*10(9)/L or platelets < 100*10(9)/L)
• NNG= 200
• Risk: 7.4% versus 7.9%
• In TPMT variant carriers:
• NNT= 5
Risk: 2.6% versus 22.9%
Intervention Control RR(95%CI)
Total(n) 399 370
Hematologicalsideeffect 29(7,2%) 29(7,8%)
TMPTvariant 1/39(2,6%) 8/35(22,9%) 0,11(0,01-0,85)
NoTPMTvariant 29/360(8,1%) 22/335(6,6%) 1,2(0,72-2,09)
• 783IBDpatients;mercaptopurineorazathioprine
• 1:1randomizedtoscreeningvsnoscreeningTPMT*2,TPMT*3A,andTPMT*3C
• HET:50%dosereduction,HOM90%dosereduction
• Primairyendpoint:leuko’s<3.0*10(9)/Lorplatelets<100*10(9)/L)
• “10-foldreductioninhematologicADRsamongvariantcarrierswithoutdifferencesin
treatmentefficacy”
Coenen MJ, Gastroenterology. 2015 907-17
ThiopurineresponseOptimizationbyPharmacogenetictesting
inInflammatoryboweldiseaseClinics
TOPICTRIAL
Farmacogenetische test aangevraagd?
• Wie heeft wel eens een farmacogenetische
test aangevraagd?
• Welke test/welk geneesmiddel?
4%
97,6% van de artsen 99,7% van de apothekers
is ervan overtuigd dat genetische variatie de reactie op een geneesmiddel kan beïnvloeden Heeft u in de afgelopen 6 maanden een farmacogenetische test aangevraagd of aanbevolen?
15%
~400 huisartsen 667 apothekers
Enquête artsen en apothekers
Stanek, CPT 2012:450-458 ; Bank, Pharmacogenomics 2017:18(3):215-225
Verkoop Verkoop
Bank, Pharmacogenomics 2017:18(3):215-225
High expectations
Willen patiënten het?
Haalbaarheid farmacogenetische
screening voor CYP2D6 en CYP2C19 in
huisartsenpraktijken
Polyfarmacie patienten; >60 jaar
Screening; geen ADE
Deelname: 58.1%
DNA extractie (Oragene®): 83.3%
Call rate:
• 93.3% CYP2D6
• 100% CYP2C19
Swen, Eur J Clin Pharmacol 2011, 8 Oct
Persoonlijk standpunt farmacogenetische tests
TPMT – thiopurines
CYP2C19 – clopidogrel
CYP2C9-VKORC1 – coumarines
DPYD – 5FU/capecitabine
HLA-B – abacavir/carbamazepine
G6PD – rasburicase
UGT1A1 – irinotecan
IL28B – pegintron
SLCO1B1 – statine + myopathie
CYP2D6 – tamoxifen
CYP3A5 - tacrolimus
44
‘If genotype is known’
Clinical Implication Score
Swen, Clin Pharmacol Ther 2018:103(5):795-801
For the 47 actionable drug-gene interactions
Examples scores
category drug-gene
essential Capecitabine-DPYD Fluorouracil-DPYD Tegafur-DPYD Irinotecan-UGT1A1
beneficial Codeine-CYP2D6 * Phenytoin-HLA-B **
potentially beneficial Tramadol-CYP2D6 Lansoprazol-CYP2C19 Omeprazol-CYP2C19 Pantoprazol-CYP2C19
* At doses of 4 dd 20 mg or higher, children >12 doses 4 dd 10 mg or higher; or Patients with additional risk factors such as CYP3A4 inhibitors or decreased Renal function ** In Asians, non-Japanese
DPWG May 2018
Farmacogenetisch lab: genotypering en advies
http://www.lumc.nl/org/kft/
Implementation study LUMC: IP3
Implementation of Pharmacogenetics in Primary care Project
• 200 patients included and pre-emptively genotyped
• Panel of genetic variants: CYP2C9; 2C19, 2D6, 3A5, DYPD, SLCO-1B1, TPMT
and VKORC1; 40 alleles
• 40 pharmacies (Leiden)
• 200 patients included
• 89.5% ≥ 1 “actionable” genotype
• 61.5 % ≥ 2
• 28.5% ≥ 3
• 9.5% ≥ 4
• 2.0% ≥ 5
• 31.0 % of patients therapeutic
recommendation; dose adjustment or
monitoring
Implementing PGx in Primary Care Project (IP3)
Adherence PGx guidelines
• >85% of the recommendations accepted
• Follow-up data being collected
8
57
3 1,5
8,5
14,5
7,5
amitriptyline
atorvastatin
citalopram
escitalopram
nortriptyline
simvastatin
venlafaxine
Drug (%)
N = 3.221.696 (Unique pat.)
First Rx* (4.138.909) Gene Phenotype Actionable#
Dose- adj. /switch**
PPI’s 1.026.441 CYP2C19 UM 41058 871
Coumarines 62.558 VKORC1 TT 10634 10634
Clopidogrel 98.709 CYP2C19 PM + IM 24677 24677
Statines 305.999 SLCO-1B1 Lage act. 78029 49024
Thiopurines 11.424 TPMT IM + PM 1828 1828
Tramadol 357.389 CYP2D6 IM + PM + UM 167972 8934
Codeine 519.728 CYP2D6 IM + PM + UM 244272 12993
TCA’s 127.804 CYP2D6 IM + PM + UM 60068 60068
Venlafaxine 26.603 CYP2D6 IM + PM 12503 11838
Flecainide 13.605 CYP2D6 IM + PM + UM 6394 680
Paroxetine 27.018 CYP2D6 IM + PM + UM 12698 675
Tamoxifen 10.807 CYP2D6 IM + PM 4809 4809
…. **based on prevalence from IP3 # based on DPWG guidelines
Impact Netherlands 2016
Case : capecitabine toxiciteit
• 15 - 30% patiënten ernstige toxiciteit (diarree, mucositis, HFS)
• 10% hiervoor opname
• 0.2-0.4% lethaal
Genotypering DPYD *1/*2A
Deenen, Ann Intern Med 2010
• Mw, 60 jr, gemetastaseerd CRC • CAPOX-B • (CAP 1000 mg/m2 2dd d1-14)
DPYD *2A: IVS14+1 G>A
DNA
mRNA
exon 13 exon 14 exon 15 5’ 3’
AG GT AG AG GT GT
>97% <3 %
GT AT
exon
13 5’ exon
14 exon
15
3’ exon
13
5’ exon
15
3’
functional DPD non-functional DPD
no DPYD*2A variant
with
DPYD*2A variant (heterozygous)
50% dose reduction normal dose
with
DPYD*2A variant (heterozygous)
normal dose
73%
28% 23%
Prospective *2A screening (n=2,038) 50% dose reduction in patients with DPYD*2A
Deenen, J Clin Oncol 2016:227-34
(literature)
DPYD @ LUMC
Oncologist considers DPYD testing
‘standard of care’
pre-therapeutic - screening
Pharmacist alerts physician if FU/CAP is prescribed with no DPYD testing.
DPWG uses ‘gene activity score’
Activity DPYD variant
0 DPYD*2A (IVS14+1G>A;c.1905+1G>A) DPYD*13 (c.1679T>G; I560S)
0,5 c.2846A>T (D949V) c.1236A>G/HapB3 (E412E)
1 DPYD*1 (wild-type)
Gene activity score % of normal dose
0 no 5FU/capecitabine
0,5 25
1 50
1,5 75
2 100
Dosing advice for: • DPYD*2A • DPYD*13 • c.2846A>T • c.1236G>A/HapB3
Henricks, 2015:Pharmacogenomics:1277-86
DPYD screening @ LUMC
Routine pre-therapeutic DPYD
screening LUMC (per april 2013)
Retrospective analysis: 314 patients
(18 maanden)
Screening:
mean: 87%
final: 90-100%
Lunenburg, Pharmacogenomics 2015;17(7):721
Implementation DYPD screening
• Pre-therapeutic screening was performed in 87% of patients, reaching 90-
100% in the last 6 months of the project
• Acceptance of dose recommendation: 90%
• Chemoradiaton
• No grade 3-4 toxicity in patients with initial dose reduction
• Grade 3-4 toxicity was only seen in DPYD variant carriers without a dose
reduction or who received a dose increase in subsequent cycles
• Dose titrations possible, guided by toxicity (not too fast)
DPYD screening is feasible in clinical practice
Lunenburg et al. Pharmacogenomics 2015;17(7):721
Nationwide - Alpe DPD study
Up front DPYD genotyping to reduce toxicity • Alpe DPD study (NCT02324452) • More SNPs (sufficient evidence for dose-adjustments for 4 SNPs) Study aim: To determine the safety, feasibility and cost-effectiveness of DPYD genotype and DPD phenotype-directed individualized dosing of fluoropyrimidines
PI’s: J. Schellens, HJ Guchelaar Lancet Oncology; 2018: 19 Oct Online
Funded by:
Update guideline colorectal cancer Medical oncologist 2017 (17-5-2017) DPYD genotyping is highly recommended prior to fluoropyrimidine treatment.
Patient inclusion
1103 included patients
1181 patients recruited
85 DPYD variant carriers
1018 wild-type patients
78 excluded patients
• Open for inclusion: April 30th 2015 – December 21st 2017
Risk of severe toxicity is decreased by DPYD genotyping
Meta-analysis/historical cohort: Meulendijks et al. Lancet Oncol 2015
Other findings: • Hospitalization risk similar between DPYD
carriers and wild-type patients in our study
• No toxicity-related deaths in patients with DPYD genotype-guided dosing
• DPYD genotyping strategy was cost-saving
Similar drug exposure in DPYD-guided and wild-type patients
Conclusions
• Upfront DPYD genotyping improves patient safety of fluoropyrimidines – This strategy is feasible in routine clinical practice and cost-saving
– For DPYD*2A and c.1679T>G carriers, a 50% initial dose reduction is adequate
– For c.1236G>A and c.2846A>T carriers, a larger dose reduction (instead of 25%) is advised
• Results endorse that implementing DPYD genotype-guided dosing is the new standard of care – Upfront genotyping and dose-individualization should be included in clinical guidelines
Simvastatine – SLCO1B1
Statines
• Myopathy
• 1:10.000 patienten per jaar
• Afhankelijk van dosis
• Gebruik andere geneesmiddelen
• ciclosporine, amiodarone
SEARCH, N Engl J Med 2008;359(8):789
Simvastatine – SLCO1B1
SEARCH: Study of the Effectiveness of Additional Reductions in
Cholesterol and Homocysteine
N=6031 N=6033
20 mg 80 mg
N=8 N=98 #myopathies
Mean follow up 6 yrs
SEARCH, N Engl J Med 2008;359(8):789
Simvastatine – SLCO1B1
DNA from
• 85 “myopathy” cases (caucasians)
• 90 controls matched for gender, age, GFR, amiodarone
Genome Wide Association Study with 300k SNP array
SEARCH, N Engl J Med 2008;359(8):789
Simvastatine – SLCO1B1
Rs4363657 (SLCO1B1)
• C-allel: 4.3 maal verhoogde
kans
• CC: 17.4 maal verhoogde kans
• 60% myopathy-gevallen
verklaard
SEARCH, N Engl J Med 2008;359(8):789
Genotypering Rx Interpretatie en advies:
ziekenhuisapotheker Geindividualiseerde
therapie
0
200
400
600
800
1000
1200
1400
1600
2008 2010 2012 2014 2016
Genotyperingen
Farmacogenetica @ LUMC
Pre-therapeutisch testen:
• Oncologie: capecitabine/5-FU: DPYD (rs3918290, rs55886062, rs67376798, rs56038477)
• Transplantatie: CYP3A5 (rs776746, rs10264272)
• Psychiatrie: patienten met therapie resistente depressie; ECT: CYP2D6 en CYP2C19
• Gastroenterologie/Hepatologie:
azathioprine/6-mercaptopurine: TPMT
(rs1800462, rs1800460, rs1142345)
Genetic counseling
• Pharmacogenetics clinic LUMC
• Clinical pharmacist & clinical geneticist
• PGx screened patients are offered genetic counseling
Example counseling patient
• I am a CYP2D6 poor metabolizer
• For which drugs is this relevant? • Is this relevant for certain food products? • Is this relevant for my children? • Can I take paracetamol safely? • Should my parents be tested? • Should I be re-tested in 5 or 10 years?
• €15 million, H2020, 10 EU countries
• Started 1 Jan 2016, 5 yr
• Reduction severe ADR: 30%
Overall aim U-PGx:
“Making actionable pharmacogenomic data and effective
treatment optimization accessible to every European citizen”
U-PGx consortium H.J. Guchelaar (Coordinator), J.J. Swen, M. Kriek
M. Pirmohamed, R. Turner J. Stingl M. Ingelman-Sundberg
C. Mitropoulou M. van Rhenen, K.C. Cheung
D. Steinberger
V.H.M. Deneer M. Samwald
G. Sunder-Plassmann A. Cambon-Thomsen
M. Karlsson S. Jonsson
G. Toffoli E. Cecchin C.L. Davila Fajardo
G. Patrinos V. Dolzan
M. Schwab E. Schaeffeler
N=8,100
Project Outline
Development of powerful and barrier-free CDSS
http://safety-code.org/
DNA-paspoort
DNA-passport: tweets…
PREPARE: Current Status
N=4,050 N=4,050
March 2017 Now
Arm Number of patients enrolled
PGx guided prescribing 2171
Standard of care 1542
TOTAL 3713
Real-time inclusion monitor
Cost-effectiveness PGx testing
Repurposing of whole exome sequencing data
• WES is routinely used for diagnosis of monogenic diseases
• Over 2000 individuals with WES data at the LUMC
• >90% form child-parent trio
• Entire exome is sequenced
Is it feasible to use existing WES data for pharmacogenetics?
Results
• 166 out of 230 individuals gave consent and have data available
• 94% of individuals were child-parents trio’s
• 5 variants, located outside of the genes/ lack of coverage:
• 1 for HLA-A*3101
• 2 or HLA-B*1502
• 1 for CYP2C19*17
• 1 for UGT1A1*28/*37
• CYP2D6 ultra-rapid
cannot be detected
Conclusie
Farmacogenetica
• is de erfelijkheid van geneesmiddel respons
• kan leiden tot veiliger en effectievere farmacotherapie
• richtlijnen zijn beschikbaar
• geintegreerd voorschrijven en afleveren van
geneesmiddelen
84