Pharmacogenomics: The Promise of Personalized Medicine Christina Aquilante, Pharm.D. Assistant Professor Department of Pharmaceutical Sciences School of.

Pharmacogenomics:Pharmacogenomics:The Promise of Personalized The Promise of Personalized

Medicine Medicine Christina Aquilante, Pharm.D.Christina Aquilante, Pharm.D.

Assistant ProfessorAssistant ProfessorDepartment of Pharmaceutical SciencesDepartment of Pharmaceutical Sciences

School of PharmacySchool of PharmacyUniversity of Colorado at Denver and Health University of Colorado at Denver and Health

Sciences CenterSciences Center

ObjectivesObjectives

Provide an overview of pharmacogenomics and Provide an overview of pharmacogenomics and its clinical relevanceits clinical relevanceDiscuss clinically-relevant examples of:Discuss clinically-relevant examples of:– Drug metabolism pharmacogenomicsDrug metabolism pharmacogenomics– Drug target pharmacogenomicsDrug target pharmacogenomics

Discuss the challenges facing Discuss the challenges facing pharmacogenomic studies and the movement of pharmacogenomic studies and the movement of pharmacogenomics into clinical practicepharmacogenomics into clinical practiceDiscuss pharmacogenomics from the FDA and Discuss pharmacogenomics from the FDA and pharmaceutical industry perspectivepharmaceutical industry perspective

Interindividual Variability in Drug Interindividual Variability in Drug ResponseResponse

DiseaseDisease Drug ClassDrug Class Rate of Poor ResponseRate of Poor ResponseAsthmaAsthma Beta-agonistsBeta-agonists 40-75%40-75%HypertensionHypertension VariousVarious 30%30%Solid CancersSolid Cancers VariousVarious 70%70%DepressionDepression SSRIs, tricyclicsSSRIs, tricyclics 20-40%20-40%DiabetesDiabetes Sulfonylureas, othersSulfonylureas, others 50%50%ArthritisArthritis NSAIDs, COX-2 inhibitorsNSAIDs, COX-2 inhibitors 30-60%30-60%SchizophreniaSchizophrenia VariousVarious 25-75%25-75%

Factors Contributing to Factors Contributing to Interindividual Variability in Drug Interindividual Variability in Drug

Disposition and ActionDisposition and ActionAgeAgeRace/ethnicityRace/ethnicityWeightWeightGenderGenderConcomitant DiseasesConcomitant DiseasesConcomitant DrugsConcomitant DrugsSocial factorsSocial factorsGENETICSGENETICS

PERSONALIZEDMEDICINE

“We wish to suggest a structure for the salt of [DNA].This structure has novel features which are of considerable biological interest.”

Human Genome ProjectHuman Genome Project

Determine the sequence of the 3 billion Determine the sequence of the 3 billion nucleotides that make up human DNAnucleotides that make up human DNA

Characterize variability in the genomeCharacterize variability in the genome

Identify all the genes in human DNAIdentify all the genes in human DNA

The Era of Genomic Medicine: The Era of Genomic Medicine: – Improve prediction of drug efficacy or toxicity Improve prediction of drug efficacy or toxicity – Improve the diagnosis of diseaseImprove the diagnosis of disease– Earlier detection of genetic predisposition to diseaseEarlier detection of genetic predisposition to disease

NewsweekJune 25, 2001

“…pharmacogeneticspromises to targettreatment to a patient’sgenetic profile…”

Genetics or Genomics?Genetics or Genomics?

PharmacogeneticsPharmacogenetics– Study of how genetic differences in a SINGLE Study of how genetic differences in a SINGLE

gene influence variability in drug response gene influence variability in drug response (i.e., efficacy and toxicity)(i.e., efficacy and toxicity)

PharmacogenomicsPharmacogenomics– Study of how genetic (genome) differences in Study of how genetic (genome) differences in

MULTIPLE genes influence variability in drug MULTIPLE genes influence variability in drug response (i.e., efficacy and toxicity)response (i.e., efficacy and toxicity)

Current Concept of Current Concept of PharmacogenomicsPharmacogenomics

Roden DM et al. Ann Intern Med 2006; 145:749-57

Potential of PharmacogenomicsPotential of Pharmacogenomics

All patients with same diagnosis

1

2Responders and patients not predisposed to toxicity

Non-respondersand toxic

responders

Treat with alternativedrug or dose

Treat with conventionaldrug or dose

Clinical RelevanceClinical Relevance

Can we predict who will derive an optimal Can we predict who will derive an optimal response?response?

Can we predict who will have a toxicity?Can we predict who will have a toxicity?

– Host (patient) genotype determines optimal Host (patient) genotype determines optimal drug therapy approachdrug therapy approach

– Disease (pathogen) genotype determines Disease (pathogen) genotype determines optimal drug therapy approachoptimal drug therapy approach

DNA is InformationDNA is Information

DNADNA

A, T, G, CA, T, G, C

CodonCodon

GeneGene

ChromosomeChromosome

GenomeGenome

ENGLISHENGLISH

Abcdefg….xyzAbcdefg….xyz

WordWord

SentenceSentence

ChapterChapter

BookBook

Composition of the Human Composition of the Human GenomeGenome

Mutation/PolymorphismMutation/Polymorphism 1 bp1 bp

Unit of genetic codeUnit of genetic code 3 bp3 bp

Coding sequence (exons)Coding sequence (exons) 3,000 bp3,000 bp

Gene (exons and introns)Gene (exons and introns) 50,000 bp50,000 bp

ChromosomeChromosome 150,000,000 150,000,000 bpbp

Human genomeHuman genome 3,000,000,000 bp3,000,000,000 bp

The Foundation of Pharmacogenomics: The Foundation of Pharmacogenomics: Differences in the Genetic Code Differences in the Genetic Code

Between PeopleBetween People

Mutation: difference in the DNA code that Mutation: difference in the DNA code that occurs in occurs in less thanless than 1% of population 1% of population– Often associated with rare diseasesOften associated with rare diseases

Cystic fibrosis, sickle cell anemia, Huntington’s diseaseCystic fibrosis, sickle cell anemia, Huntington’s disease

Polymorphism: difference in the DNA code that Polymorphism: difference in the DNA code that occurs in occurs in more thanmore than 1% of the population 1% of the population– A single polymorphism is less likely to be the main A single polymorphism is less likely to be the main

cause of a diseasecause of a disease– Polymorphisms often have no visible clinical impactPolymorphisms often have no visible clinical impact

Single Nucleotide Polymorphisms Single Nucleotide Polymorphisms (SNP)(SNP)

Pronounced “snip”Pronounced “snip”

Single base pair difference in the DNA Single base pair difference in the DNA sequencesequence– Over 2 million SNPs in the human genomeOver 2 million SNPs in the human genome

Other polymorphisms:Other polymorphisms:– Insertion/deletion polymorphismsInsertion/deletion polymorphisms– Gene duplicationsGene duplications– Gene deletionsGene deletions

Consequences of PolymorphismsConsequences of Polymorphisms

May result in a different amino acid or stop May result in a different amino acid or stop codon codon

May result in a change in protein function May result in a change in protein function or quantityor quantity

May alter stability of mRNAMay alter stability of mRNA

No consequence No consequence

Genetics TerminologyGenetics Terminology

AllelesAlleles = different = different DNA sequences at a DNA sequences at a locuslocus– Codon 389 Codon 389 11-AR-AR

Arg (0.75)Arg (0.75)

Gly (0.25)Gly (0.25)

GenotypeGenotype = pair of = pair of alleles a person has alleles a person has at a region of the at a region of the chromosomechromosome– Codon 389 Codon 389 11-AR-AR

Arg389Arg Arg389Arg

Arg389Gly Arg389Gly

Gly389Gly Gly389Gly

Genetics TerminologyGenetics Terminology

Phenotype: outward manifestation of a Phenotype: outward manifestation of a traittrait

Linkage: measure of proximity of 2 or Linkage: measure of proximity of 2 or more polymorphisms on a single more polymorphisms on a single chromosomechromosome– Polymorphisms in close proximity tend to be Polymorphisms in close proximity tend to be

co-inheritedco-inherited– Regions of linked polymorphisms are known Regions of linked polymorphisms are known

as haplotypesas haplotypes

Haplotype MapHaplotype MapFor specific locations in the genome, a For specific locations in the genome, a small number of SNP patterns small number of SNP patterns (haplotypes) can account for 80-90% of (haplotypes) can account for 80-90% of entire human populationentire human population

International HapMap Project:International HapMap Project:– Identifying common haplotypes in four Identifying common haplotypes in four

populations from different parts of the worldpopulations from different parts of the world– Identifying “tag” SNPs that uniquely identify Identifying “tag” SNPs that uniquely identify

these haplotypesthese haplotypes

PharmacogenomicsPharmacogenomics

DRUGTARGETS

DRUGMETABOLIZING

ENZYMES

DRUGTRANSPORTERS

PHARMACOKINETICSPHARMACODYNAMICS

Variability in Efficacy/Toxicity

Johnson JA. Trends in Genetics 2003: 660-666

Drug Metabolism Drug Metabolism PharmacogenomicsPharmacogenomics

Evidence of an inherited basis for drug Evidence of an inherited basis for drug response dates back in the literature to the response dates back in the literature to the 1950s1950s– Succinylcholine: 1 in 3000 patients Succinylcholine: 1 in 3000 patients

developed prolonged muscle relaxationdeveloped prolonged muscle relaxation

MonogenicMonogenic

Phenotype to genotype approachPhenotype to genotype approach

Drug Metabolizing EnzymesDrug Metabolizing Enzymes

Examples of Drug Metabolism Examples of Drug Metabolism PharmacogenomicsPharmacogenomics

NEJM 2003; 348: 529-537

Examples of Drug Metabolism Examples of Drug Metabolism PharmacogenomicsPharmacogenomics

NEJM 2003; 348: 529-537

Warfarin and CYP2C9Warfarin and CYP2C9

Widely prescribed anticoagulant drug used to Widely prescribed anticoagulant drug used to prevent blood clotsprevent blood clotsNarrow range between efficacy and toxicityNarrow range between efficacy and toxicityLarge variability in the dose required to achieve Large variability in the dose required to achieve therapeutic anticoagulationtherapeutic anticoagulation– Doses vary 10-fold between peopleDoses vary 10-fold between people

CYP2C9 is the enzyme responsible for the CYP2C9 is the enzyme responsible for the metabolism of warfarinmetabolism of warfarinSNPs exist in CYP2C9 gene that decrease the SNPs exist in CYP2C9 gene that decrease the activity of the CYP2C9 metabolizing enzymeactivity of the CYP2C9 metabolizing enzyme

CYP2C9 Polymorphisms and CYP2C9 Polymorphisms and Warfarin DoseWarfarin Dose

Warfarin dose is affected by CYP2C9 genotypeWarfarin dose is affected by CYP2C9 genotype

Gage BF et al. Thromb Haemost 2004; 91: 87-94

*2 and *3 are SNPs

CYP2C9 Genotype and Bleeding EventsCYP2C9 Genotype and Bleeding Events

Compared to wild-type, CYP2C9 variants Compared to wild-type, CYP2C9 variants had a higher risk of serious or life-had a higher risk of serious or life-threatening bleedsthreatening bleeds

Hazard Ratio of 3.94 during the first 3 Hazard Ratio of 3.94 during the first 3 months of follow-upmonths of follow-up

Hazard Ratio of 2.39 for the entire follow-Hazard Ratio of 2.39 for the entire follow-up periodup period

Higashi et al. JAMA 2002; 287

WT

Variant

Challenges Facing Warfarin Challenges Facing Warfarin PharmacogenomicsPharmacogenomics

Despite the strong association between Despite the strong association between CYP2C9 genotype and warfarin dose, CYP2C9 genotype and warfarin dose, CYP2C9 genotype accounts for only a CYP2C9 genotype accounts for only a small portion of the total variability in small portion of the total variability in warfarin doses (~10-20%)warfarin doses (~10-20%)

Need to determine other genetic and Need to determine other genetic and non-genetic factors that contribute to non-genetic factors that contribute to interindividual variability in warfarin dosesinterindividual variability in warfarin doses

CYP2D6 PolymorphismsCYP2D6 Polymorphisms

CYP2D6 is responsible for the metabolism of a CYP2D6 is responsible for the metabolism of a number of different drugsnumber of different drugs– Antidepressants, antipsychotics, analgesics, Antidepressants, antipsychotics, analgesics,

cardiovascular drugscardiovascular drugs

Over 100 polymorphisms in CYP2D6 have been Over 100 polymorphisms in CYP2D6 have been identifiedidentifiedBased on these polymorphisms, patients are Based on these polymorphisms, patients are phenotypically classified as:phenotypically classified as:– Ultrarapid metabolizers (UMs)Ultrarapid metabolizers (UMs)– Extensive metabolizers (EMs)Extensive metabolizers (EMs)– Poor metabolizers (PMs)Poor metabolizers (PMs)

CYP2D6 PhenotypesCYP2D6 PhenotypesNEJM 2003; 348:529

Roden DM et al. Ann Intern Med 2006; 145:749-57

CYP2D6 Polymorphisms and CYP2D6 Polymorphisms and Psychiatric Drug ResponsePsychiatric Drug Response

Increased rate of adverse effects in poor Increased rate of adverse effects in poor metabolizers due to increased plasma metabolizers due to increased plasma concentrations of drug:concentrations of drug:– Fluoxetine (ProzacFluoxetine (Prozac) death in child attributed ) death in child attributed

to CYP2D6 poor metabolizer genotypeto CYP2D6 poor metabolizer genotype– Side effects of antipsychotic drugs occur more Side effects of antipsychotic drugs occur more

frequently in CYP2D6 poor metabolizersfrequently in CYP2D6 poor metabolizers– CYP2D6 poor metabolizers with severe CYP2D6 poor metabolizers with severe

mental illness had more adverse drug mental illness had more adverse drug reactions, increased cost of care, and longer reactions, increased cost of care, and longer hospital stayshospital stays

CYP2D6 and CodeineCYP2D6 and Codeine

Codeine requires activation by CYP2D6 in Codeine requires activation by CYP2D6 in order to exert its analgesic effectorder to exert its analgesic effect

Due to genetic polymorphisms, 2-10% of Due to genetic polymorphisms, 2-10% of the population cannot metabolize codeine the population cannot metabolize codeine and are resistant to the analgesic effectsand are resistant to the analgesic effects

Interindividual variability exists in the Interindividual variability exists in the adequacy of pain relief when uniform adequacy of pain relief when uniform doses of codeine are givendoses of codeine are given

StratteraStrattera® ® (Atomoxetine)(Atomoxetine)

Treatment of attention deficit hyperactivity Treatment of attention deficit hyperactivity disorderdisorder– CYP2D6 poor metabolizers have 10-fold higher CYP2D6 poor metabolizers have 10-fold higher

plasma concentrations to a given dose of plasma concentrations to a given dose of STRATTERA compared with extensive STRATTERA compared with extensive metabolizers metabolizers

– Approximately 7% of Caucasians are poor Approximately 7% of Caucasians are poor metabolizers metabolizers

– Higher blood levels in poor metabolizers may Higher blood levels in poor metabolizers may lead to a higher rate of some adverse effects of lead to a higher rate of some adverse effects of STRATTERASTRATTERA

CYP2C19 and Proton Pump CYP2C19 and Proton Pump InhibitorsInhibitors

Proton pump inhibitors are used to treat Proton pump inhibitors are used to treat acid reflux and stomach ulcersacid reflux and stomach ulcersUlcer cure rates using omeprazole and Ulcer cure rates using omeprazole and amoxicillin by CYP2C19 phenotype:amoxicillin by CYP2C19 phenotype:

Cure RateCure Rate– Rapid metabolizersRapid metabolizers 28.6%28.6%– Intermediate metabolizersIntermediate metabolizers 60%60%– Poor metabolizersPoor metabolizers 100%100%

Furuta, T. et. al. Ann Intern Med 1998;129:1027-1030

Roche AmpliChip: FDA-ApprovedRoche AmpliChip: FDA-Approved

Roche AmpliChip P450 TestRoche AmpliChip P450 Test

The Roche AmpliChip CYP450 Test is intended to identify a patient's CYP2D6 and CYP2C19 genotype from genomic DNA extracted from a whole blood sample.

Information about CYP2D6 and CYP2C19 genotype may be used as an aid to clinicians in determining therapeutic strategy and treatment dose for therapeutics that are metabolized by the CYP2D6 or CYP2C19 gene product.

Thiopurine-S-Methyltransferase (TPMT)Thiopurine-S-Methyltransferase (TPMT)

Thiopurine drugs are used to treat cancerThiopurine drugs are used to treat cancer– Acute lymphoblastic leukemiaAcute lymphoblastic leukemia

TPMT is important for metabolizing thiopurinesTPMT is important for metabolizing thiopurines– azathioprine, mercaptopurine (6-MP)azathioprine, mercaptopurine (6-MP)

Polymorphisms in the TPMT gene result in Polymorphisms in the TPMT gene result in decreased TPMT enzyme activitydecreased TPMT enzyme activity

Decreased TPMT activity predisposes Decreased TPMT activity predisposes individuals to severe, life-threatening toxicities individuals to severe, life-threatening toxicities from these drugsfrom these drugs

Variability in TPMT ActivityVariability in TPMT Activity

Enzyme Activity Levels in 300 Caucasian Patients

0102030405060708090

100

low medium high

TPMT Enzyme Activity

% o

f S

ub

ject

s

Genotype-Guided 6-MP DosingGenotype-Guided 6-MP Dosing

Pharmacogenomics 2002;3(1):89-98.

6-Mercaptopurine Prescribing 6-Mercaptopurine Prescribing InformationInformation

There are individuals with an inherited deficiencyof the enzyme thiopurine methyltransferase(TPMT) who may be unusually sensitive to themyelosuppressive effects of mercaptopurine andprone to developing rapid bone marrowsuppression following the initiation of treatment.

Substantial dosage reductions may be required toavoid the development of life-threatening bonemarrow suppression in these patients.

Imuran Prescribing InformationImuran Prescribing Information

TPMT genotyping or phenotyping can be used to identify patients with absent or reduced TPMT activity.

Patients with low or absent TPMT activity are at an increased risk of developing severe, life-threatening myelotoxicity from IMURAN if conventional doses are given.

Physicians may consider alternative therapies for patients who have low or absent TPMT activity (homozygous for non-functional alleles). IMURAN should be administered with caution to patients having one non-functional allele (heterozygous) who are at risk for reduced TPMT activity that may lead to toxicity if conventional doses are given. Dosage reduction is recommended in patients with reduced TPMT activity.

TPMT and ThioguaninesTPMT and Thioguanines

Clinical implications:Clinical implications:– Genetic testing for TPMT is routine practice at Genetic testing for TPMT is routine practice at

some cancer centers for protocols involving some cancer centers for protocols involving thiopurine drugs thiopurine drugs

– CLIA approved test availableCLIA approved test available– Implications for cancer, transplant, rheumatoid Implications for cancer, transplant, rheumatoid

arthritis, lupus, dermatology, and Crohn’s arthritis, lupus, dermatology, and Crohn’s disease treatmentdisease treatment

Drug Target Drug Target PharmacogenomicsPharmacogenomics

Drug Target PharmacogenomicsDrug Target Pharmacogenomics

Direct protein target of drug Direct protein target of drug – ReceptorReceptor– EnzymeEnzyme

Proteins involved in pharmacologic response Proteins involved in pharmacologic response – Signal transduction proteins or downstream proteinsSignal transduction proteins or downstream proteins

Polymorphisms associated with Polymorphisms associated with disease risk disease risk – ““Disease-modifying” polymorphismsDisease-modifying” polymorphisms– ““Treatment-modifying” polymorphismsTreatment-modifying” polymorphisms

POLYGENICPOLYGENIC

Complexity of Drug EffectComplexity of Drug Effect

Assessing Phenotype in Drug Target Assessing Phenotype in Drug Target PharmacogenomicsPharmacogenomics

Depression—Symptom rating scalesDepression—Symptom rating scales– Indirect measure of drug responseIndirect measure of drug response– Inter-rater reliabilityInter-rater reliability

Hypertension—Blood pressureHypertension—Blood pressure– Minute to minute and diurnal variabilityMinute to minute and diurnal variability– Influence of environmental factors (e.g. lack of Influence of environmental factors (e.g. lack of

rest before measurement)rest before measurement)

Diabetes—Blood glucoseDiabetes—Blood glucose– Diurnal variation in blood glucoseDiurnal variation in blood glucose– Influence of environmental factors (e.g. Influence of environmental factors (e.g.

diet/exercise)diet/exercise)

ComparisonComparisonDrug Metabolism PgxDrug Metabolism Pgx

Polymorphisms often lead Polymorphisms often lead to non-functional or to non-functional or absent proteinsabsent proteins

Distinct phenotypes Distinct phenotypes – Bimodal/trimodal Bimodal/trimodal

distributiondistribution

Phenotypes are easily Phenotypes are easily measured measured – Drug concentrationDrug concentration– In vitro catalytic activityIn vitro catalytic activity

Drug Target PgxDrug Target Pgx

Polymorphisms usually Polymorphisms usually don’t result in lack of don’t result in lack of protein functionprotein function– ““Subtle” effectsSubtle” effects

Differences in Differences in phenotypes are smallerphenotypes are smaller

Measurement of Measurement of phenotypes is difficultphenotypes is difficult– Imprecise and variableImprecise and variable

Failure to consider Failure to consider haplotypeshaplotypes

Johnson JA and Lima JJ. Pharmacogenetics 2003; 13:525-534

Examples of Drug Target Examples of Drug Target PharmacogenomicsPharmacogenomics

Evans WE. NEJM 2003; 348:538-48

Examples of Disease or Treatment Examples of Disease or Treatment Modifying PharmacogenomicsModifying Pharmacogenomics

Evans WE. NEJM 2003; 348:538-48

Beta-blockers and Beta-blockers and Hypertension (HTN)Hypertension (HTN)

HTN is the most prevalent chronic disease in the HTN is the most prevalent chronic disease in the US and a contributor to morbidity and mortalityUS and a contributor to morbidity and mortalityBeta-blockers are first-line agent in the treatment Beta-blockers are first-line agent in the treatment of HTNof HTNMarked variability in response to beta-blockers Marked variability in response to beta-blockers – 30-60% of patients fail to achieve adequate blood 30-60% of patients fail to achieve adequate blood

pressure lowering with beta-blockerspressure lowering with beta-blockers

Common beta-blockers used in HTN: Common beta-blockers used in HTN: – Metoprolol Metoprolol – AtenololAtenolol

Podlowski, et al. J Mol Med 2000;78:90.

Beta-1 Adrenergic ReceptorBeta-1 Adrenergic Receptor

Codon 49 SerGly

Codon 389ArgGly

Beta-1 Receptor Polymorphisms Beta-1 Receptor Polymorphisms and Response to Metoprololand Response to Metoprolol

Johnson JA et al. Clin Pharmacol Ther 2003; 74:44-52

Beta-2 Adrenergic Receptor Beta-2 Adrenergic Receptor Polymorphisms and Response to Polymorphisms and Response to

Albuterol in AsthmaAlbuterol in AsthmaHyperreactivity of the airways is the hallmark of Hyperreactivity of the airways is the hallmark of asthmaasthmaAirway smooth muscle contains beta-2 receptors Airway smooth muscle contains beta-2 receptors that produce broncodilationthat produce broncodilationAlbuterol is a beta-2 agonist that is used in the Albuterol is a beta-2 agonist that is used in the treatment of asthmatreatment of asthma– Produces smooth muscle cell relaxation and Produces smooth muscle cell relaxation and

bronchodilationbronchodilation

Forced expiratory volume in 1 second (FEVForced expiratory volume in 1 second (FEV11))– Phenotypic measure of responsePhenotypic measure of response

Beta-2 Polymorphisms and Beta-2 Polymorphisms and Response to AlbuterolResponse to Albuterol

Lima JJ. Clin Pharmacol Ther 1999; 65:519-25

•Single 8 mg albuterol dose

•Albuterol-evoked increases in FEV1 were higher and more rapid in Arg16 homozyotes compared with Gly carriers

• Codon 16 polymorphism is a determinant of bronchodilator response to albuterol

Lima JJ et al. Clin Pharmacol Ther 1999; 65: 519-25

VKOR and WarfarinVKOR and Warfarin

Warfarin works by inhibiting Vitamin K Epoxide Warfarin works by inhibiting Vitamin K Epoxide Reductase (VKOR) Reductase (VKOR) VKOR helps recycle vitamin K which is VKOR helps recycle vitamin K which is important in proper functioning of clotting important in proper functioning of clotting factorsfactorsBy inhibiting VKOR, warfarin alters the vitamin By inhibiting VKOR, warfarin alters the vitamin K cycle and results in the production of inactive K cycle and results in the production of inactive clotting factors clotting factors Polymorphisms exist in the gene for VKOR Polymorphisms exist in the gene for VKOR (VKORC1)(VKORC1)

VKORC1 Genotype and Warfarin VKORC1 Genotype and Warfarin Dose RequirementsDose Requirements

VKORC1 3673 Genotype

Mea

n W

arfa

rin D

ose

(mg

per

wee

k)

0

10

20

30

40

50

60

70

33 mg/wk

46 mg/wk

21 mg/wk

G/G G/A A/A

Warfarin PharmacogenomicsWarfarin Pharmacogenomics

CYP2C9 SNPs account for a small amount of CYP2C9 SNPs account for a small amount of variability in warfarin doses (~10%)variability in warfarin doses (~10%)

VKORC1 SNPs explain a larger portion of VKORC1 SNPs explain a larger portion of variability in warfarin doses (~20-25%)variability in warfarin doses (~20-25%)

Almost 50% of variability in warfarin doses can Almost 50% of variability in warfarin doses can be explained by a combination of factors:be explained by a combination of factors:– VKORC1 SNPsVKORC1 SNPs– CYP2C9 SNPsCYP2C9 SNPs– Non-genetic factors (age, weight, concomitant drugs, Non-genetic factors (age, weight, concomitant drugs,

concomitant disease states)concomitant disease states)

Warfarin PharmacogenomicsWarfarin Pharmacogenomics

Current Status:Current Status:– Develop and validate dosing algorithms to Develop and validate dosing algorithms to

that include VKORC1 genetic information, that include VKORC1 genetic information, CYP2C9 genetic information, and non-genetic CYP2C9 genetic information, and non-genetic factors (e.g., age, weight, concomitant drugs, factors (e.g., age, weight, concomitant drugs, concomitant disease states)concomitant disease states)

– Test if dosing warfarin based on genotype is Test if dosing warfarin based on genotype is better than the “usual” care approachbetter than the “usual” care approach

Abacavir HypersensitivityAbacavir Hypersensitivity

Antiretroviral used for treatment of HIVAntiretroviral used for treatment of HIV5% of patients experience hypersensitivity 5% of patients experience hypersensitivity reactions to the drugreactions to the drug– Hypersensitivity is fatal in rare casesHypersensitivity is fatal in rare cases

Hypersensitivity reaction starts with severe GI Hypersensitivity reaction starts with severe GI symptoms, followed by fever and rashsymptoms, followed by fever and rashDiscontinuation of drug reverses symptomsDiscontinuation of drug reverses symptomsRe-challenge of abacavir in hypersensitive Re-challenge of abacavir in hypersensitive individuals can result in life-threatening low individuals can result in life-threatening low blood pressure or deathblood pressure or death

Lancet 2002;359:727-32.Lancet 2002;359:727-32.

Abacavir HypersensitivityAbacavir Hypersensitivity

Hypersensitivity typically believed to be an Hypersensitivity typically believed to be an immunologic reactionimmunologic reaction

Hypersensitivity might be genetically Hypersensitivity might be genetically linked, and thus predictablelinked, and thus predictable

Major histocompatibility proteins (MHC) Major histocompatibility proteins (MHC) investigated because of known links in investigated because of known links in other immune responses and allergic other immune responses and allergic reactionsreactions

Genetics of Abacavir HypersensitivityGenetics of Abacavir Hypersensitivity

• Patients with the HLA-B*5701 variant were 117 times more likely to be hypersensitive to abacavir than those who did not have the variant

• 13 patients had 3 linked genetic variants (*5701, DR7, DQ3) and all patients were abacavir hypersensitive

•All abacavir hypersensitive patients were Caucasian, thereforestudies in other racial groups are needed

Western HIV Australia HIV Cohort Study

Disease Risk PolymorphismsDisease Risk Polymorphisms

Polymorphisms can predispose individuals to a Polymorphisms can predispose individuals to a disease or increase the risk for diseasedisease or increase the risk for disease

If a drug with a known adverse effect is given to If a drug with a known adverse effect is given to a person with a genetic susceptibility to that a person with a genetic susceptibility to that adverse effect, there is an increased likelihood adverse effect, there is an increased likelihood for that adverse effectfor that adverse effect

Clotting Factor Polymorphisms, Blood Clotting Factor Polymorphisms, Blood Clots, and Oral Contraceptive PillsClots, and Oral Contraceptive Pills

Polymorphisms exist in clotting factor genesPolymorphisms exist in clotting factor genes

Oral contraceptive pills alone are associated with Oral contraceptive pills alone are associated with an increased risk of blood clotsan increased risk of blood clots

Women who have clotting factor polymorphisms Women who have clotting factor polymorphisms are at an even greater risk for blood clots if they are at an even greater risk for blood clots if they receive oral contraceptive pillsreceive oral contraceptive pills

Oral Contraceptive Pills and Blood ClotsOral Contraceptive Pills and Blood Clots

Martinelli I. Pharmacogenetics 2003; 13:589-594

Patients on OCP who are homozygous for Factor V Leiden have 50 to100-fold increased risk of VTE

Het

eroz

ygot

es

A Different Aspect ofA Different Aspect of Drug Target Pharmacogenomics Drug Target Pharmacogenomics

In all of the examples thus far, the drug target In all of the examples thus far, the drug target has been a human proteinhas been a human proteinThe gene encoding that human protein has The gene encoding that human protein has generally NOT undergone mutation during the generally NOT undergone mutation during the patient’s lifepatient’s lifeHowever, in the areas of infectious diseases and However, in the areas of infectious diseases and cancer, the drug target is often a non-human cancer, the drug target is often a non-human protein protein – Cancer: Tumor DNACancer: Tumor DNA– Infectious Diseases: Viral genotype Infectious Diseases: Viral genotype

e.g., HIV, HBV, HCVe.g., HIV, HBV, HCV

HER-2 Protein and HerceptinHER-2 Protein and Herceptin

Herceptin (trastuzumab): Herceptin (trastuzumab): – Metastatic breast cancerMetastatic breast cancer– Targets tumor cells that over-Targets tumor cells that over-

express the human epidermal express the human epidermal growth factor receptor 2 growth factor receptor 2 (HER2) protein(HER2) protein

– Best response attained in Best response attained in women who over-express the women who over-express the HER2 proteinHER2 protein

– HER-2 over-expression in HER-2 over-expression in breast cancer cells should be breast cancer cells should be done before patients receive done before patients receive the drugthe drug

Herceptin: Prescribing InformationHerceptin: Prescribing Information

HERCEPTIN (Trastuzumab) as a single agent is HERCEPTIN (Trastuzumab) as a single agent is indicated for the treatment of patients with indicated for the treatment of patients with metastatic breast cancer whose tumors metastatic breast cancer whose tumors overexpress the HER2 protein and who have overexpress the HER2 protein and who have received one or more chemotherapy regimens received one or more chemotherapy regimens for their metastatic disease. for their metastatic disease.

HERCEPTIN should be used in patients whose HERCEPTIN should be used in patients whose tumors have been evaluated with an assay tumors have been evaluated with an assay validated to predict HER2 protein validated to predict HER2 protein overexpression overexpression

Hepatitis CHepatitis C

Interferon-Interferon--2b and ribavirin are used to treat -2b and ribavirin are used to treat patients with hepatitis C viruspatients with hepatitis C virus

Different mutations exist in the hepatitis C virusDifferent mutations exist in the hepatitis C virus

Knowledge of a person’s hepatitis C genotype Knowledge of a person’s hepatitis C genotype may help play a role in the therapeutic decision-may help play a role in the therapeutic decision-making processmaking process

HIV and Antiretroviral DrugsHIV and Antiretroviral Drugs

Resistance to antiretroviral agents hinders Resistance to antiretroviral agents hinders the management of HIV diseasethe management of HIV disease

In the virus, mutations occur which confer In the virus, mutations occur which confer drug resistancedrug resistance

Knowledge of viral genotype (or Knowledge of viral genotype (or phenotype) can help guide the selection of phenotype) can help guide the selection of antiretroviral therapyantiretroviral therapy

Challenges Facing the Field of Challenges Facing the Field of PharmacogenomicsPharmacogenomics

Multiple studies, but literature is inconclusive in Multiple studies, but literature is inconclusive in some instancessome instances

Genetics accounts for an insufficient percentage Genetics accounts for an insufficient percentage of response variability for a given drugof response variability for a given drug

Few studies documenting genotype-guided Few studies documenting genotype-guided therapy is better than the “usual care” approachtherapy is better than the “usual care” approach

Few “point-of-care” tests available to determine Few “point-of-care” tests available to determine a person’s genetic make-up or protein a person’s genetic make-up or protein expressionexpression

Potential Reasons for Potential Reasons for DiscrepanciesDiscrepancies

Inadequately powered studiesInadequately powered studies

Studying different drug response phenotypesStudying different drug response phenotypes

Studying different patient populations Studying different patient populations (differences in allele frequencies)(differences in allele frequencies)

Problems precisely measuring phenotypeProblems precisely measuring phenotype

Subtlety of functional effects of polymorphismsSubtlety of functional effects of polymorphisms

Focus on single SNPs instead of haplotypesFocus on single SNPs instead of haplotypes

Failure to consider the complexity of drug Failure to consider the complexity of drug responseresponse

Johnson JA and Lima JJ. Pharmacogenetics 2003; 13:525-534

Pharmacogenetics and Pharmacogenetics and Pharmacogenomics Knowledge Base Pharmacogenomics Knowledge Base

(PharmGKB)(PharmGKB)

Publicly accessible knowledge basePublicly accessible knowledge base– www.pharmgkb.orgwww.pharmgkb.org

Goal: establish the definitive source of Goal: establish the definitive source of information about the interaction of genetic information about the interaction of genetic variability and drug responsevariability and drug response1.1. Store and organize primary genotyping dataStore and organize primary genotyping data2.2. Correlate phenotypic measures of drug response Correlate phenotypic measures of drug response

with genotypic datawith genotypic data3.3. Curate major findings of the published literatureCurate major findings of the published literature4.4. Provide information about complex drug pathwaysProvide information about complex drug pathways5.5. Highlight genes that are critical for understanding Highlight genes that are critical for understanding

pharmacogenomicspharmacogenomics

Role of Pharmacogenomics in the Role of Pharmacogenomics in the Drug Development ProcessDrug Development Process

80% of products that enter the development 80% of products that enter the development pipeline pipeline FAILFAIL to make it to market to make it to market

Pharmacogenomics may contribute to a Pharmacogenomics may contribute to a “smarter” drug development process“smarter” drug development process– Allow for the prediction of efficacy/toxicity during Allow for the prediction of efficacy/toxicity during

clinical developmentclinical development– Make the process more efficient by decreasing the Make the process more efficient by decreasing the

number of patients required to show efficacy in clinical number of patients required to show efficacy in clinical trialstrials

– Decrease costs and time to bring drug to marketDecrease costs and time to bring drug to market

Pharmacogenomic Paradigm in the Pharmacogenomic Paradigm in the Drug Development ProcessDrug Development Process

Current Options Options with Pharmacogenomics

Pro

por

tion

of

pat

ien

ts s

how

ing

poo

r or

no

resp

onse

Low

High

Continue clinical trialsto market

Abandon drugbefore market

Optimize clinical trials,making them

smaller and shorter

Continue trials safelyby excluding at-risk pts

Personalized Medicine and the Personalized Medicine and the Pharmaceutical IndustryPharmaceutical Industry

Targeted Therapies:Targeted Therapies:– Herceptin: treatment of HER2 positive metastatic Herceptin: treatment of HER2 positive metastatic

breast cancerbreast cancer– Gleevec: treatment for patients with Philadelphia Gleevec: treatment for patients with Philadelphia

chromosome-positive chronic myeloid leukemiachromosome-positive chronic myeloid leukemia– Erlotinib: treatment for non-small cell lung cancerErlotinib: treatment for non-small cell lung cancer

Most effective in epidermal growth factor receptor positive Most effective in epidermal growth factor receptor positive tumorstumors

– Maraviroc (not approved): treatment for HIVMaraviroc (not approved): treatment for HIVStudies have incorporated a screening process for different Studies have incorporated a screening process for different receptors that HIV uses to gain access to cellsreceptors that HIV uses to gain access to cells

– Iloperidone (not approved): schizophrenia treatmentIloperidone (not approved): schizophrenia treatmentCompany identified a genetic marker that predicts a good Company identified a genetic marker that predicts a good response to the drugresponse to the drug

Pharmacogenomic Paradigm in the Pharmacogenomic Paradigm in the Pharmaceutical IndustryPharmaceutical Industry

Rare side effectprediction

Efficacy prediction

Market expansion

Common side effectprediction

FDA and PharmacogenomicsFDA and PharmacogenomicsTraditionally, industry has been hesitant to Traditionally, industry has been hesitant to submit pharmacogenomic data due to fears of:submit pharmacogenomic data due to fears of:– Delays in drug developmentDelays in drug development– Request for additional clinical studiesRequest for additional clinical studies– Potentially put clinical trials on holdPotentially put clinical trials on hold

FDA published: “Draft Guidance for Industry: FDA published: “Draft Guidance for Industry: Pharmacogenomic Data Submission” in 2003. Pharmacogenomic Data Submission” in 2003. (currently under revision)(currently under revision)

Set criteria for Voluntary Genomic Data Set criteria for Voluntary Genomic Data Submission (VGDS)Submission (VGDS)

http://www.fda.gov/cder/guidance/5900dft.pdf

Pharmacogenomics Information in Pharmacogenomics Information in the Published Literaturethe Published Literature

Zineh I et al. Ann Pharmacother. 2006; 40: 639-44

Pharmacogenomics Information in Pharmacogenomics Information in FDA-Approved Prescribing InformationFDA-Approved Prescribing Information

Zineh I et al. Pharmacogenomics J; 2004: 1-5

Moving Pharmacogenomics to Moving Pharmacogenomics to Clinical PracticeClinical Practice

Identify sequence variability in candidate genes

In vitro functional studies

Proof-of-concept clinical studies

Studies that mimic clinical practice

Documenting sufficient variability to predict clinical utility

Document Pgx superiority: Pgx-guided versus usual care

Johnson JA. Trends in Genetics 2003; 19: 660-66

The Future of PharmacogenomicsThe Future of Pharmacogenomics

Genome wide approach versus candidate gene Genome wide approach versus candidate gene approachapproachThousands of SNPsThousands of SNPsThousands of patientsThousands of patientsReplication studiesReplication studiesSophisticated databases housing pharmacogenomic Sophisticated databases housing pharmacogenomic informationinformationDrug selection and dosing algorithms incorporating Drug selection and dosing algorithms incorporating non-genetic and genetic informationnon-genetic and genetic informationPoint of care genetic testingPoint of care genetic testing

"Here's my

sequence..."

The New Yorker

““Personalized medicine: Personalized medicine: elusive dreamelusive dream or or imminent realityimminent reality??

In summary: it is bothIn summary: it is both.”.”

Larry Lesko, Director of the FDA Larry Lesko, Director of the FDA Office of Clinical Pharmacology Office of Clinical Pharmacology

and Biopharmaceuticsand Biopharmaceutics

Clin Pharmacol Ther; 2007: 807-816Clin Pharmacol Ther; 2007: 807-816