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