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Pharmacogenomics in Clinical Practice

Indiana Institute of Personalized MedicineIndiana University School of Medicine

Division of Clinical Pharmacology

An Introduction to Clinical Pharmacogenomics

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Objectives A case… A fundamental change in the medical paradigm A short primer on pharmacogenomics

◦ SNPs◦ Metabolism and transport◦ SNP nomenclature

Some pharmacogenomically important medications Clinical application

◦ Back to the case…

Introduction to Clinical Pharmacogenomics

Originally created for IU Provider CME 9/2013 3

Case: RF is a 58 year-old female with a past medical history

of coronary artery disease, hypertension, and hypercholesterolemia who presents to her cardiologist with shortness of breath, and a sensation of a “racing heart”. Electrocardiogram confirms atrial fibrillation. Included in RF’s treatment plan is oral anticoagulation initiation with warfarin. ◦ RF agrees to genetic screening for potential variants that

could affect her warfarin therapy Results reveal that she has the heterozygous CYP2C9*2/*3 and

the GA VKORC1 genotype

Clinical Case


Current Medical Paradigm…

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Current Medical Paradigm

D I S E A S E

Patient Outcome?MEDICATI

ON


Patient outcomes…◦Mitigate or cure disease◦No effect ◦Adverse drug event, difficult to predict Sometimes serious

Current Medical Paradigm


Pharmacogenomic Medical Paradigm…

Clinical Pharmacogenomic Paradigm

Patient Outcome

-Mitigate or cure disease-No serious adverse drug events

“Personalized Medicine”

Pharmacogenetic test


Historical milestones • Hemolysis in World War II African-American soldiers treated with primaquine

lead to identification of G6PD deficiency

• In the 1957, Kalow and Gunn discovered subjects homozygous for a gene encoding an atypical form of pseudocholinesterase had delayed recovery from succinylcholine

• 1959, Vogel et al. a common genetic variation in the hepatic enzyme N-acetyltransferase was found to cause marked differences in drug half-life and plasma concentration of isoniazid

• 1977, Eichelbaum et al. identified the CYP2D6 polymorphism

• 2001, Drucker et al. demonstrated remarkable response using imatinib for CML

• 2003, finished version of human genome sequence is completed

• June 13th, 2013, US Supreme Court rules that human genes cannot be patented

Clinical Pharmacogenomics Milestones


A primer on clinical pharmacogenomics…

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99.5% of the genome between any two individuals is identical

Mutations that occur in genomic DNA give rise to genetic variation◦ When a mutation occurs in at least 1% of individuals in a

population it is termed a “polymorphism”◦ Most common polymorphism is the single nucleotide

polymorphism or “SNP” Occurs when there is a difference in a single nucleotide Approximately 90% of all genetic variation is thought to derive from

SNPs 2/3rd of SNPs involve replacement of cytosine for thymine ~10 million SNPs in the human genome, so far…

◦ Much of the research has focused on the characterization of the SNPs in human genes regulating drug disposition Drug metabolizing enzymes Intracellular transport of drugs

Clinical Pharmacogenomics: A Primer


Drug metabolism◦ Two basic metabolic reactions

Phase 1 metabolism: Cytochrome P450 (CYP450) system CYP3A, 2D6, 2C9, 2C19 Mixed-function oxidases produce more polar compounds

Phase 2 metabolism: N-acetyltransferase, UDP-glucoruoronysltransferase (UGT),

glutathione S-transferase Conjugation reactions increase the molecular weight, increases

bulkiness of compounds



Clinical Pharmacogenomics: A Primer Drug transporters are

found in liver, kidney, intestines, brain and pancreas Two major classes

Uptake Facilitate translocation of drugs into

cells OAT (organic anion transporter)

SLCO1B1 OCT (organic cation transporter)

Efflux Excrete drugs from within cells to

extracellular space P-gp (p-glycoprotein), MRP2,

MRP3

Nature Reviews Drug Discovery 9, 215-236 (March 2010) | doi:10.1038/nrd3028

Giacomini KM et al. Nature Rev Drug Discovery, 2010; 9: 215-236

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Drug metabolism and transport◦SNPs can change the protein of a

CYP450 enzyme or transporter• Leads to altered drug metabolism and/or

transport• Effects on drug disposition leading to unpredictable

pharmacodynamics• Drug response?• Adverse drug event?

Clinical Pharmacogenomics: A primer


Nomenclature of SNPs◦ Phase 1 enzymes:

CYP2C9*2A

◦ Alleles are alternate versions of a gene◦ *1 allele designation (CYP2C9*1) most commonly refers to the “wild type” or

“normal” enzyme◦ *2 or greater denote polymorphic alleles and are typically numbered in order

of discovery-validation Homozygous designation: CYP2C9*1/*1 (two copies of wild-type allele) Heterozygous designation: CYP2C9*1/*2 (one copy of wild-type and one copy of

reduced function allele)


Superfamily

Family

Individual Member

Subfamily

Suballele

Allele


Nomenclature of SNPs

◦ Phase 2 enzymes and transporters Utilizes similar nomenclature

UGT1A1*1/*1 (homozygous for wild-type) SLCO1B1*1/*5 (heterozygous, contains one functional and one reduced function allele, “C”

allele)◦ Still other nomenclatures…

Named by haplotype VKORC1, “haplotype A”, (G1639A)

GG, homozygous, (wild-type), normal levels of VKORC1 GA, heterozygous, lower level of VKORC1 AA, homozygous, lowest levels of VKORC1

Named by allele SLCO1B1*5 “C” high myopathy risk allele, “T” other, low myopathy risk alleles

TT, homozygous, (low myopathy risk) CT, heterozygous, (moderate myopathy risk) CC, homozygous, (high myopathy risk)

Human Leukocyte Antigen (HLA) HLA-B*5701



Some pharmacogenomically important medications…

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Clopidogrel◦ Pro-drug, requires CYP2C19 metabolism to become active◦ CYP2C19 SNPs have been identified leading to different

metabolism phenotypes CYP2C19* 1 (wild-type), normal functioning enzyme CYP2C19*17, ultra-rapid metabolizer CYP19*2, CYP19*3, CYP2C19*4 have little or no functioning enzyme

24% Caucasian, 33% African-Americans, 50% of Asians have at least one loss-of-function allele

In 227 cardiac patients, Shuldiner et al. found that 21% of clopidogrel subjects with CYP2C19 LOF SNPs reached study endpoint (death, non-fatal MI, urgent revascularization) compared with 10% without the LOF SNPs

Clinical Pharmacogenomics: Important Medications

Shuldiner AR et al, JAMA, 2009; 302 (8): 849-57.


Warfarin◦ Consists of two isomers, S- and R-warfarin

S-warfarin is more potent and metabolized by CYP2C9 R-warfarin is metabolized by CYP1A1, 1A2 and 3A4 Pharmacologic target is VKORC1

◦ Important SNPs CYP2C9*1 (wild type): extensive metabolizers CYP2C9*2 and *3: poor metabolizers

Heterozygous CYP2C9*1/*2 or *3: 20-40% lower clearance Homozygous CYP2C9*2/*2: 50% lower clearance Homozygous CYP2C9*3/*3: 85% lower

clearance CYP2C9 SNPs account for ~10-12% of the interindividual variability

CYP2C9*2: 16% of Caucasians, 1% of Asians and African–Americans CYP2C9*3: 7% of Caucasians, 2% of Asians and African-Americans



Warfarin◦ Pharmacologic target of warfarin is also polymorphic

Vitamin K 2,3-epoxide reductase (VKORC1), inhibitory target of warfarin VKORC1 GG, wild-type VKORC1 GA, need ~25% lower doses VKORC1 AA, need ~50% lower doses

VKORC1 SNPs account for ~25% of the interindividual variability Haplotype A: African-Americans 15%, Caucasians 42%, Asians 90%

◦ CYP2C9 and VKORC1 variants have been estimated to explain 30-35% of the variability in warfarin dose requirements



Warfarin◦ Recent study by Anderson et al. compared two

groups initiated on warfarin therapy PG-guided: CYP2C9 and VKORC1 genotype

incorporated into a warfarin dosing algorithm, n=504 Parallel controls: Standard of care, n=1,866

◦ Investigators found significantly less INRs out-of-range (OOR) and more time in therapeutic range (TTR) during the critical 1 to 3 months of warfarin therapy in the PG-guided compared to control PG-guided group also had significantly lower

numbers of serious adverse events (thromboembolism, hemorrhage, death)

◦ Several large trials are underway to investigate this further Genetics Informatics Trial of Warfarin to Prevent DVT (GIFT) Clarification of Optimal Anticoagulation Through Genetics

(COAG) European Pharmacogenetics of Anticoagulant Therapy-

Warfarin (EU-PACT)


Anderson J L et al. Circulation 2012;125:1997-2005

Percentage of OOR INRs and % TTR for PG-guided dosing algorithms and parallel (standard dosing) controls.

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Simvastatin◦ Drug transporters also have

SNPs◦ OATP1B1 is a transporter for

entry of simvastatin into the hepatocyte for metabolism SLCO1B1 is the gene that encodes

this transporter◦ A genetic variant of SLCO1B1

(C allele) was found to be associated with an increased risk of statin-induced myopathy in a study of over 12,000 subjects taking simvastatin


SEARCH Collaborative Group, NEJM 2008;359:789-99

22Originally created for IU Provider CME 9/2013Originally created for IU Provider CME 9/2013

Tamoxifen◦ Pro-drug metabolized by CYP2D6 to active endoxifen

CYP2D6*1, CYP2D6*2 (normal or “extensive” metabolizers) Poor metabolizers (PM) CYP2D6*3, *4, *5, *6 Intermediate metabolizers (heterozygotes)

One normal and one PM allele (CYP2D6*1/*3) Ultra-rapid metabolizers

3 or more copies of normal alleles due to duplication CYP2D6*1/*2/*2

PMs are found in 7-14% of Caucasians, 14.5% of African-Americans◦ In a study of early stage breast cancer subjects taking tamoxifen,

Schroth et al. found that the presence of 2 functional CYP2D6 alleles was associated with better clinical outcomes than those subjects with non-functional or reduced-function CYP2D6 alleles


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Schroth W et al, JAMA, 2009; 302(13): 1429-36


Abacavir◦ Associated with a non-

specific “hypersensitivity reaction” in patients with the HLA-B*5701 allele Fever, rash, constitutional

symptoms, GI and respiratory symptoms that worsen with continued dosing Symptoms abate when abacavir

is discontinued In US, HLA-B*5701 is found in

8% of Caucasians, 2.5% of African-Americans and ~1% of Asians


24Originally created for IU Provider CME 9/2013Originally created for IU Provider CME 9/2013

Prior examples are only a subset of the medications with pharmaco-genomic disposition issues

A 2011 list of the top 200 prescribed medications by total prescriptions included 17 with pharmacogenomic information in their FDA package inserts◦ Includes the 5th and 7th most commonly prescribed medications◦ In 2011, 362 million prescriptions were filled for these 17

medications◦ Numbers are only expected to increase as pharmacogenomics

and personalized medicine grows

Clinical PharmacogenomicsImportant Medications


Interesting, but so what?

How do I utilize this genetic information for the

patient in my clinic?

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Clinical Pharmacogenetics Implementation Consortium (CPIC)• Purpose of CPIC is to “translate genetic information into clinical actions and to

make recommendations for actionable pharmacogenetic variants”• Group of clinical pharmacologists, clinicians and scientists that review all

current literature and develop recommendations and algorithms to guide drug dosing based on pharmacogenotypes

CPIC prioritizes gene-drug pairs based on community input and sponsored surveys of the CPIC members, American Society of Clinical Pharmacology and Therapeutics (ASCPT) and the public

• CPIC is a frequent contributor to the FDA and endorsed by the AMA, ASHP• CPIC has evaluated 14 drugs so far with more to follow

Abacavir, allopurinol, azathioprine, capecitabine, carbamazepine, clopidogrel, codeine, irinotecan, mercaptopurine, phenytoin, simvastatin, TCAs, thioguanine, warfarin

Clinical Application of Pharmacogenomics


Now, back to our case…

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Case: RF is a 58 year-old female with a past medical history

of coronary artery disease, hypertension, and hypercholesterolemia who presents to her cardiologist with shortness of breath, and a sensation of a “racing heart”. Electrocardiogram confirms atrial fibrillation. Included in RF’s treatment plan is oral anticoagulation initiation with warfarin. ◦ RF agrees to genetic screening for potential variants that

could affect her warfarin therapy Results reveal that she has the heterozygous CYP2C9*2/*3 and

the GA VKORC1 genotype

Clinical Case


CPIC guideline for warfarin:Recommended daily warfarin doses (mg/day) to achieve a therapeutic INR based onCYP2C9 and VKORC1 genotype using the warfarin product insert approved by the US Food and Drug Administration

Clinical Case revisited…

Reproduced from updated warfarin (Coumadin) product label.

VKORC1(1639G>A)

CYP2C9*1/*1(mg)

CYP2C9*1/*2(mg)

CYP2C9*1/*3(mg)

CYP2C9*2/*2(mg)

CYP2C9*2/*3(mg)

CYP2C9*3/*3(mg)

GG 5-7 5-7 3-4 3-4 3-4 0.5-2

GA 5-7 3-4 3-4 3-4 0.5-2 0.5-2

AA 3-4 3-4 0.5-2 0.5-2 0.5-2 0.5-2

Clin Pharmacol Ther, 2011, 90: 625-29.Originally created for IU Provider CME 9/2013 30

Clinical Pharmacogenomics Conclusions Pharmacogenomic medicine is a

powerful tool to inform drug selection and clinical decision-making◦ Has demonstrated potential to improve

efficacy and safety of medications As more clinical data emerges

and genotyping costs fall, there will be increasing utilization and presence in clinical medicine

"Here's my sequence...”

New Yorker magazine


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