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Cancer Pharmacogenetics: Lessons Learned. Geoffrey Liu, MD FRCPC Scientist, OCI. Currently Approved Oncology Drugs. Cost of Colorectal Cancer Treatment Per 6 Months ($). Meropol NJ, Schulman KA. Cost of Cancer Care: Issues and Implications. J Clin Oncol 2007 25:180-186. - PowerPoint PPT Presentation
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Cancer Pharmacogenetics: Cancer Pharmacogenetics: Lessons LearnedLessons Learned
Geoffrey Liu, MD FRCPC
Scientist, OCI
Currently Approved Oncology DrugsCurrently Approved Oncology Drugs
Cost of Colorectal Cancer Treatment Cost of Colorectal Cancer Treatment Per 6 Months ($)Per 6 Months ($)
Meropol NJ, Schulman KA. Cost of Cancer Care: Issues and Implications. J Clin Oncol 2007 25:180-186.
NY Times, September 2, 2009
Personalized MedicinePersonalized Medicine
Tailoring medical prevention and treatment Tailoring medical prevention and treatment therapies to the characteristics of each patient therapies to the characteristics of each patient improving their quality of life and health improving their quality of life and health outcome.outcome.
"The right medicine to the right person at the "The right medicine to the right person at the right dosage at the right time" right dosage at the right time"
• PharmacoepidemiologyPharmacoepidemiology• Pharmacogenomics Pharmacogenomics
"Here's my
sequence...”
New Yorker
Personalized or Predictive MedicinePersonalized or Predictive Medicine
Patients with same diagnosisRespond to treatment
No response to treatment
Experience adverse events
Personalized/Stratified/
Predictive Medicine
What Disciplines are Involved?
Bioinformatics
Molecularbiology
BioethicsBioStatistics
Cancer Pharmacogenomics (PGx)Cancer Pharmacogenomics (PGx) The study of how variation in an The study of how variation in an
individual’s germline and/or tumor individual’s germline and/or tumor genome are related to their metabolism genome are related to their metabolism and physiological response to drugs and physiological response to drugs used in cancer treatmentused in cancer treatment• Single Nucleotide Polymorphisms (substitutions)Single Nucleotide Polymorphisms (substitutions)• Insertions and deletionsInsertions and deletions• Copy number VariationsCopy number Variations• Methylation patternsMethylation patterns• Molecular biomarkersMolecular biomarkers• Gene expressionGene expression
Cancer Pharmacogenetics
Cancer Pharmacogenomics
Biomarkers Predictive for Drug Outcomes
Biomarkers Predictive for Treatment Outcomes
Cancer Pharmacogenetics
Cancer Pharmacogenomics
Biomarkers Predictive for Drug Outcomes
Biomarkers Predictive for Treatment Outcomes
GERMLINE
SOMATIC or TUMOUR
PROTEINS, IMAGING
RADIATION THERAPY
Gene Mutations — Inherited or Acquired
Hereditary (germline) mutations
• alterations in DNA inherited from a parent and are found in the DNA of virtually all of your cells.
Acquired (somatic) mutations
• alterations in DNA that develop throughout a person’s life
Somatic Examples
Her2neu and Herceptin in breast ca KRAS and EGFR MoAbs in colorectal ca EGFR activating mutations and EGFR TKIs in
NSCLC ?ALK-EML4 translocation and ALK-targeting ?BRAF mutations and BRAF inhibitor in
melanoma
(inherited) Genetic Variations?(inherited) Genetic Variations?
Substitutions (or SNPs)Substitutions (or SNPs) InsertionsInsertions DeletionsDeletions DuplicationsDuplications Short repeatsShort repeats Gene deletionsGene deletions Copy Number VariationCopy Number Variation
Gene and Gene and Protein Protein Expression Expression Levels/FunctionLevels/Function/Regulation/Regulation
Polymorphisms can alter function through multiple mechanisms
Promoter Exon UTRsIntron
Conformational changeBinding site changeEarly termination
Polymorphisms can alter function through multiple mechanisms
Promoter Exon
UTRs
UTRsIntron
“junk areas”microRNAsMeta-regulators
Regions that are spliced into non-coding RNAs
mRNATransport guidance
Pharmacodynamics (PD): the study of the biochemical and physiological effects of drugs and the mechanisms of drug action and the relationship between drug concentration and effect (Drug effect on the body)
Pharmacokinetics (PK): the study of the time course of substances and their relationship with an organism or system (Journey of drugs)• Absorption• Distribution• Metabolism• Excretion
Every aspect may affect the final drug effect
Pharmacology
Pharmacogenetics
The Study of the genetics of factors related to PD and PK
Genes involved in PD Drug mechanism of action. targets/downstream effectors
Genes involved in PK Drug Absorption/Transport Activation/Metabolism/Excretion
Drug Genetic Variation Mech’m Outcome
5FU/analogue DPD PK Toxicity
6MP and AZA TPMT PK Toxicity
Irinotecan UGT1A1 PK Toxicity
Aromatase Inhibitors
TCL1 PD? Toxicity
Warfarin CYP2C9 & VKORC1 PK & PD Toxicity
Cisplatin TPMT and COMT Unclear Toxicity
Tamoxifen CYP2D6 PK Efficacy
5FU/analogue TS PK Toxicity
5FU/analogue MTHFR PK Toxicity
Cyclophosphamide CYPs PK Eff & Tox
MoAbs Fc-gamma-RII & III PD Efficacy
EGFR TKIs EGFR, ABCG2 PD Eff & Tox
Cisplatin DNA repair SNPs PD Eff & Tox
Dasatinib CYP3A4/3A5 PK Eff & Tox
Leve
l of
Evi
denc
e
Adapted from Coate et al, JCO, 2010)
High
Candidate Genetic Factors Candidate Genetic Factors Determining Drug ResponseDetermining Drug Response
Polymorphisms inPolymorphisms in
• Drug Receptors/Targets Drug Receptors/Targets Beta-2ARBeta-2AR
• Drug Transporters Drug Transporters MDR1MDR1
• Drug Metabolizing Enzymes Drug Metabolizing Enzymes CYP2D6CYP2D6
Goal of Pharmacogenetics
Optimize Therapy So Benefits Outweigh the Risks
Methodological Approaches
Biological Pathway-defined Epidemiological Association Studies
In vitro and In vivo Human tissue and Clinical Information
Issues to consider with Epidemiological
Association Studies Tumour vs Blood = which is your target tissue? When do you believe an association study
biomarker result?• Multiple comparisons? • Heterogeneity (of disease, of patients, of clinical
scenario) = humans are not mice; how are these things controlled?
• Biological Grounding/Functional Data?• Study Design and Study Population issues = if I
choose the “right” controls, I will always be able to find a statistically significant result
Three Common Genetic and Epidemiological Approaches
Germline• Candidate-Gene
• Genome-Wide Association (GWAS)
• Candidate-Pathway
Candidate-Gene ApproachCandidate-Gene Approach
Typically genetic variants are selected Typically genetic variants are selected based on their known physiologic or based on their known physiologic or pharmacologic effect on disease or drug pharmacologic effect on disease or drug responseresponse
Three Cancer Examplesof candidate polymorphism approaches
Irinotecan and UGT1A1 polymorphisms
Tamoxifen and CYP2D6 polymorphisms
EGFR tyrosine kinase inhibitors and EGFR polymorphisms
Three Cancer Examplesof candidate polymorphism approaches
Irinotecan and UGT1A1 polymorphisms
Tamoxifen and CYP2D6 polymorphisms
EGFR tyrosine kinase inhibitors and EGFR polymorphisms
EACH TO ILLUSTRATE SPECIFIC ISSUES
WITH ASSOCIATION STUDIES
Irinotecan metabolism and its toxicity
LeukopeniaThrombocytopenia
Anemia
Cytochrome P450 3A family
(UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily
Bone MarrowIntestine
Diarrhea
carboxylesterase 1, 2
ATP-binding cassette transporters (ABC gene family)Help drug transfer into hepatic cell membrane
SN-38+Glucuronide
Irinotecan metabolism and its toxicity
LeukopeniaThrombocytopenia
Anemia
Cytochrome P450 3A family
(UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily
Bone MarrowIntestine
Diarrhea
carboxylesterase 1, 2
ATP-binding cassette transporters (ABC gene family)Help drug transfer into hepatic cell membrane
SN-38+Glucuronide
Irinotecan metabolism and its toxicity
LeukopeniaThrombocytopenia
Anemia
Cytochrome P450 3A family
(UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily
Bone MarrowIntestine
Diarrhea
carboxylesterase 1, 2
ATP-binding cassette transporters (ABC gene family)Help drug transfer into hepatic cell membrane
SN-38+Glucuronide
Irinotecan metabolism and its toxicity
LeukopeniaThrombocytopenia
Anemia
Cytochrome P450 3A family
(UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily
Bone MarrowIntestine
Diarrhea
carboxylesterase 1, 2
ATP-binding cassette transporters (ABC gene family)Help drug transfer into hepatic cell membrane
SN-38+Glucuronide
Irinotecan metabolism and its toxicity
LeukopeniaThrombocytopenia
Anemia
Cytochrome P450 3A family
(UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily
Bone MarrowIntestine
Diarrhea
carboxylesterase 1, 2
ATP-binding cassette transporters (ABC gene family)Help drug transfer into hepatic cell membrane
SN-38+Glucuronide
UGT1A1Genotype
Innocenti et al, JCO, 2004
UGT1A1Genotype
Less functional allele
UGT1A1Genotype
Less functional allele
Protein structure of UGT1A family
540 AA, 28 signal AA, ~243 common AA in different isoforms
Signal peptide
Functional part
~269AA~243 AA28AAN C
Protein structure of UGT1A family
540 AA, 28 signal AA, ~243 common AA in different isoforms
Signal peptide
Functional part
~269AA~243 AA28AA
TM
Protein structure of UGT1A family
540 AA, 28 signal AA, ~243 common AA in different isoforms
Signal peptide
Functional part
~269AA~243 AA28AA
UGT1A gene family: Alternative Splicing Variants
Important Genetic Variations for UGT1A1
Allele name Protein
PromoterNucleotide
change
Coding nucleotide change Amino acid change
UGT1A7*1a UGT1A7.1 G115, N129, R131, W208
UGT1A7*1b UGT1A7.1 -70(G>A)
UGT1A7*2 UGT1A7.2 387(T>G)/391(C>A)/392(G>A) ( K129, k131) N129K/R131K
UGT1A7*3 UGT1A7.3387(T>G)/391(C>A)/392(G>A)/ 622(T>C); (k129,
K131,R208)N129K/R131K/W208R
UGT1A7*4 UGT1A7.4 622(T>C) (R208) W208R
UGT1A7*5 UGT1A7.5 343(G>A) G115S
UGT1A7*6 UGT1A7.6 417(G>C) E139D
UGT1A7*7 UGT1A7.7 387(T>G)/391(C>A)/392(G>A)/417(G>C) N129K/R131K/E139D
UGT1A7*8 UGT1A7.8 387(T>G)/391(C>A)/392(G>A)/417(G>C)/622(T>C)N129K/R131K/E139D/
W208R
UGT1A7*9 UGT1A7.9 343(G>A)/387(T>G)/391(C>A)/392(G>A) G115S/N129K/R131K
UGT1A7*10 UGT1A7.10 386(A>G)/387(T>G)/391(C>A)/392(G>A)/622(T>C) N129R/R131K/W208R
UGT1A7*11 UGT1A7.11 392(G>A) R131Q
UGT1A7*12 UGT1A7.12 -57(T>G) 622(T>C)/760(C>T) W208R/R254X
UGT1A7*13 UGT1A7.13 828(C>A) N276K
UGT1A7*14 UGT1A7.14 422(G>C) C141S
UGT1A7 allele nomenclature and important SNPs
UGT1A9 allele nomenclature and important SNPs
Variations across UGT1A polymorphisms
2 3 4 5A 5BUGT1A1
UGT1A1*6rs4148323
UGT1A1*28rs8175347
Chr234333883-Chr23433633=250bp
UGT1A1*93-3156G>A
rs10929302
UGT1A1*60-3279T>Grs4124874
Chr2:234330521-Chr2:234330398=123bp
Chr2, 234245202
Chr234255266-Chr234255944=678bp
UGT1A7
622T>C W208Rrs176832
387T>G N129Krs176832
-57 T>Grs7586110
UGT1A7 *1*2*3*4*5*6*7*8*9*10
*11*12*14
UGT1A9
UGT1A9*22-118T9/T10rs3832043
391C>A(rs17863778), 392G>A(rs17868324)
R131K342 G>A G115S()
Current Situation
UGT1As much more complex than initially thought
Additional polymorphisms involved in determining metabolism of irinotecan
Despite FDA labeling change, UGT testing is currently not being used widespread.
Current Situation
UGT1As much more complex than initially thought
Additional polymorphisms involved in determining metabolism of irinotecan
Despite FDA labeling change, UGT testing is currently not being used widespread.
CLINICAL UTILITY?
Take-Home Message:Heterogeneity and Complexity of Associations affect Results
That is why you get difference association studies that state that red meat is good, neutral or bad for you….
…but don’t throw the baby out with the bathwater
Training-Test Paradigmin Human Samples
Training Set (correct for multiple comparisons)
Multiple Validation Sets
From Bench to Bedside:Complexity of the Human Being
Biomarkers related to the host
Clinical Outcomes-Hard outcomes (OS/DFS)-Soft outcomes (toxicity/QOL)
Biomarkers of tumor
Environmental Modifying Factors
Treatment Factors
PsychosocialCultural, Economic
Non-causal Prognostic Factors
Causal Prognostic Factors
Adapted from Liu et al, 2006
From Bench to Bedside:Complexity of the Human Being
Biomarkers related to the host
Clinical Outcomes-Hard outcomes (OS/DFS)-Soft outcomes (toxicity/QOL)
Biomarkers of tumor
Environmental Modifying Factors
Treatment Factors
PsychosocialCultural, Economic
Non-causal Prognostic Factors
Causal Prognostic Factors
Adapted from Liu et al, 2006Pharmacogenetics
Tamoxifen Metabolism
Clinical Cancer Research January 2009 15; 15
Tamoxifen Metabolism
Clinical Cancer Research January 2009 15; 15
Tamoxifen Metabolism
Clinical Cancer Research January 2009 15; 15
Tamoxifen Metabolism
Clinical Cancer Research January 2009 15; 15
CYP2D6
Meyer. Nature Review 2004
CYP2D6
Meyer. Nature Review 2004
CYP2D6 Genotype and Endoxifen
0
20
40
60
80
100
120
140
160
180
Wt/Wt Wt/*4 *4/*4
Jin Y et al. JNCI;97:30, 2005
CYP2D6*4 (most common genetic variant associated with the CYP2D6 poor metabolizer state)
P<0.001, r2=0.24
Plasma Endoxifen
(nM)
0
20
40
60
80
100
0 2 4 6 8 10 12
Relapse-Free Survival
CP1229323-16
%
Years after randomization
2-year RFSEM 98%IM 92%PM 68%
Log RankP=0.009
EM
IM
PM
n=115
n=40
n=16
Goetz et al. Breast Cancer Res Treat. 2007
Relapse-Free Survival
CP1234316-3
0
20
40
60
80
100
0 2 4 6 8 10 12
%
Years after randomization
P=0.007
Extensive
Decreased
n=115
n=65
Goetz et al. Breast Cancer Res Treat. 2007
Validation?
Follow-up studies have had variable results• Not as clear cut
CYP2D6 is inducible and inhibited by many drugs• including anti-depressants and SSRIs
Many of these drugs have been used to ameliorate peri-menopausal symptoms induced by Tamoxifen
Tamoxifen and CYP2D6 CYP2D6 associated with BC outcome
• Goetz et al. 2005, 2007 (USA)• Schroth et al. 2007 (Germany)• Kiyotani et al. 2008 (Japan)• Newman et al. 2008 (UK)• Xu et al. 2008 (China)• Okishiro et al. 2009 (Japan)• Ramon et al. 2009 (Spain)• Bijl et al. 2009 (Netherlands)
CYP2D6 not associated with BC outcome• Wegman et al. 2005, 2007 (Sweden)• Nowell et al. 2005 (USA)• Goetz et al. 2009 (international consortia, n=2800)
Tamoxifen complexities
Tamoxifen
Tamoxifen active metabolites
Inactive Metabolites
CYP2D6CYP3A
SULT1A1
Tamoxifen complexities
Tamoxifen
Tamoxifen active metabolites
Inactive Metabolites
Side Effects
CYP2D6CYP3A
SULT1A1
compliance
Tamoxifen complexities
Tamoxifen
Tamoxifen active metabolites
Inactive Metabolites
CYP inhibitory agents
Side Effects
Treatment of Side Effects=
CYP2D6CYP3A
SULT1A1
compliance
Tamoxifen complexities
Tamoxifen
Tamoxifen active metabolites
Inactive Metabolites
CYP inhibitory agents
Side Effects
Treatment of Side Effects=
CYP2D6CYP3A
SULT1A1
compliance
Take-Home Messages: Confounders Play Key Roles in
Association StudiesProper Phenotyping Critical
Importance of accounting for variables and of choosing reliable
and accurate clinical endpoints
Pharmacogenetic Example: Pharmacogenetic Example: EGFR polymorphisms and EGFR TKIs (2004-)
Review of existing PK/PD/PG data In silico and bioinformaticdetermination of best targets
Haploview/Tagger
SIFT/PolyPhen/Coddle
SNP - HapMap
I2D/PPI Networks
Proprietary PK data
PGRN and public source PK/PG/PD data
Pharmacogenetic Example: Pharmacogenetic Example: EGFR polymorphisms and EGFR TKIs (2004-)
Functional Assays
LuciferasePromoterAssays
HaplotypeConstructsand functionalBinding andExpression assays
Promoter AnalysisAMPL
Gene Expression/Binding AssaysCollaboration with A. Adjei(Mayo/RPCI)
Identification of key targets to test in patient samples
Liu et al, CR 2005
CADR and-216G/T combined: PFS
RED BLUE
S/S+T/- L/-+G/G
N (%) 64 (70%) 28 (30%)
Med PFS 3.9 mos 2.0 mos
Adj. HR 0.60 reference
95%CI (0.36-0.98)
Logrank p=0.0006
Progression-free Survival (months)
Pro
ba
bili
ty
0 12 24 36 48
0%
20%
40%
60%
80%
100%
Liu et al, TPJ 2007
Phase II Study of Gefitinib In NSCLC
CADR and-216G/T combined: OS
S/S+T/- L/-+G/G
N (%) 64 (70%) 28 (30%)
Med OS 12.0 mos 7.6 mos
Adj. HR 0.60 reference
95%CI (0.36-1.00)
Logrank p=0.02
Overall Survival (months)
Pro
ba
bili
ty
0 12 24 36 48
0%
20%
40%
60%
80%
100%
Liu et al, TPJ 2007
Prospective Validation?
FISH+
FISH-
PRE
REGISTRATION
RANDOMIZATION
Erlotinib 150 mg PO daily
Pemetrexed 500mgIV D1
Erlotinib 150 mg PO daily
Pemetrexed 500mgIV D1
*21 day cycles
EGFRFISH
status
Stratification
CLINICAL
OUTCOME
Stratification factors:ECOG PS: 0/1/2Cooperative GroupStage: IIIB/IVGender: M/FSmoking Status: Never/≤15py/> 15py RECIST with re-staging q2 cycles
Until PD or toxicity or withdrawal
Schema
FISH+
FISH-
PRE
REGISTRATION
RANDOMIZATION
Erlotinib 150 mg PO daily
Pemetrexed 500mgIV D1
Erlotinib 150 mg PO daily
Pemetrexed 500mgIV D1
*21 day cycles
EGFRFISH
status
Stratification
CLINICAL
OUTCOME
Stratification factors:ECOG PS: 0/1/2Cooperative GroupStage: IIIB/IVGender: M/FSmoking Status: Never/≤15py/> 15py RECIST with re-staging q2 cycles
Until PD or toxicity or withdrawal
XClosed due to poor accrual
Mutation Testing First Line
Retrospective Validation?
The NCIC CTG study, BR.21
double-blind randomized trial of erlotinib versus placebo as second/third line treatment in Stage IIIB/IV NSCLC.
No blood collected = tiny small biopsies collected.
Results
Normal tissue (± tumor) DNA was extracted from 242/731 enrolled patients.
Genotyping success rates exceeded 92%.
In a 30 patient subset, genotyping concordance rates were >93% between normal and corresponding tumor tissue DNA.
Results
Individuals without tissue for genotyping:• were more likely to be Asian• had greater PR/CR rates• were more likely to have 2+ prior treatment
regimens• and had longer time to randomization
Subgroups of genotyped and non-genotyped patients had OS/PFS and benefited similarly from study treatment.
Issues
Too small a sample? Skewed non-representative population?
Perhaps differences between erlotinib and gefitinib
BR.19 analysis (also underpowered) RTOG 0436 – years away BIBW2772 – pending, but different drug
Take-Home Message: Validation Key to Accepting Association Study Results;
Validation not so easy…1. Training Set Validation/Test Sets
2. Biological or Functional Validation
Three Examples for Discussion
Candidate Gene Example
Genome-Wide Association Genome-Wide Association Study (GWAS) ApproachStudy (GWAS) Approach
Examines common genetic variations for a Examines common genetic variations for a role in drug response by genotyping large role in drug response by genotyping large sets of genetic variations across genomesets of genetic variations across genome
• ““Discovery-based” vs. “hypothesis-based”Discovery-based” vs. “hypothesis-based”• Relate genetic variations to clinical outcomeRelate genetic variations to clinical outcome• Identify associations in genes not previously Identify associations in genes not previously
suspected suspected
Pathway-based ApproachPathway-based Approach
Examines biologically plausible Examines biologically plausible associations between certain individual associations between certain individual polymorphisms and clinical outcomes polymorphisms and clinical outcomes
Usually combines 2+ related genetic Usually combines 2+ related genetic variants to reveal otherwise undetectable variants to reveal otherwise undetectable effects of individual variants on clinical effects of individual variants on clinical outcome.outcome.
What have we learned?
Training and Validation Sets important Control sample important (Prognostic vs
Predictive) GWAS and Pathway analyses may
improve chances of finding important and novel associations
If Phenotype is carefully measured, chances improve in finding association (e.g. clinical trial data)
Where do we go from here?
Cancer Patients
Germline / Somatic Genotype
Prediction of Drug Efficacy
Incorrect Genotype
Assignment
• Improved Outcomes
• Enhanced Response
• Minimize Toxicity Harms of
Subsequent Management
Options
Treatment Decisions
Analytic
Validity
Clinical Validity Clinical Utility
Overarching Question
Prediction of Metabolism
Prediction of Adverse Drug
Reactions
Analytic Framework + Key Questions for Evaluating Genomic Tests in a Specific Clinical Scenario
Cancer Patients
Germline / Somatic Genotype
Prediction of Drug Efficacy
Incorrect Genotype
Assignment
• Improved Outcomes
• Enhanced Response
• Minimize Toxicity Harms of
Subsequent Management
Options
Treatment Decisions
Analytic
Validity
Clinical Validity Clinical Utility
Overarching Question
Prediction of Metabolism
Prediction of Adverse Drug
Reactions
Analytic Framework + Key Questions for Evaluating Genomic Tests in a Specific Clinical Scenario
Cancer Patients
Germline / Somatic Genotype
Prediction of Drug Efficacy
Incorrect Genotype
Assignment
• Improved Outcomes
• Enhanced Response
• Minimize Toxicity Harms of
Subsequent Management
Options
Treatment Decisions
Analytic
Validity
Clinical Validity Clinical Utility
Overarching Question
Prediction of Metabolism
Prediction of Adverse Drug
Reactions
Analytic Framework + Key Questions for Evaluating Genomic Tests in a Specific Clinical Scenario
Cancer Patients
Germline / Somatic Genotype
Prediction of Drug Efficacy
Incorrect Genotype
Assignment
• Improved Outcomes
• Enhanced Response
• Minimize Toxicity Harms of
Subsequent Management
Options
Treatment Decisions
Analytic
Validity
Clinical Validity Clinical Utility
Overarching Question
Prediction of Metabolism
Prediction of Adverse Drug
Reactions
Analytic Framework + Key Questions for Evaluating Genomic Tests in a Specific Clinical Scenario
UGT1A1 and IrinotecanDPD and 5FU
√ X√
Cancer Patients
Germline / Somatic Genotype
Prediction of Drug Efficacy
Incorrect Genotype
Assignment
• Improved Outcomes
• Enhanced Response
• Minimize Toxicity Harms of
Subsequent Management
Options
Treatment Decisions
Analytic
Validity
Clinical Validity Clinical Utility
Overarching Question
Prediction of Metabolism
Prediction of Adverse Drug
Reactions
Analytic Framework + Key Questions for Evaluating Genomic Tests in a Specific Clinical Scenario
Tamoxifen and CYP2D6Cisplatin and ototoxicity; AIs and MSK toxicity
√ ?√
Cancer Patients
Germline / Somatic Genotype
Prediction of Drug Efficacy
Incorrect Genotype
Assignment
• Improved Outcomes
• Enhanced Response
• Minimize Toxicity Harms of
Subsequent Management
Options
Treatment Decisions
Analytic
Validity
Clinical Validity Clinical Utility
Overarching Question
Prediction of Metabolism
Prediction of Adverse Drug
Reactions
Analytic Framework + Key Questions for Evaluating Genomic Tests in a Specific Clinical Scenario
FC-gamma-RVEGFR2
?√
Summary Germline pharmacogenetic studies have changed
patient management in several diseases• Cancer included
In cancer, effects can be related to efficacy or toxicity, related to either PK or PD relationships
Studies in patient populations require consideration of confounders (e.g. enzyme induction/inhibition) and interactions (drug-drug)
Current research involves candidate gene, candidate pathway, or agnostic genome-wide evaluations• Next Gen Sequencing coming soon
Validation, validation, validation
Blatant Plug
AMP-PEL (Liu lab)Applied Molecular Profiling-
Pharmacogenomic Laboratory
Clinico-EpidemiologicalResearch: DescriptiveAnd Analytical
EpidemiologicalMethods Research
Biomarker Research:Cancer ManagementPreventionScreening and Early Detection
In vivo and In vitroPharmacogenomic And Radiogenomic Research
Companion ResearchFor Clinical Trials
Health Outcomes and Knowledge Translation Research
DRY LAB WET LAB
Study Name Tissue Sample Phase Drug/Tx
BR.10 (Lung) FFPE III Cisplatin
HN.6 (Head & Neck) Blood III Cisplatin and XRT
Panitumumab
BR.21 (Lung) FFPE/slides or blocks
III Erlotinib
BR.19 (Lung) FFPE III Gefitinib
BR.24 (Lung) Blood III Cediranib
TORCH (Lung) Blood III Erlotinib
MA.31 (Breast) Blood III Her2neu/EGFR
CO.17 (Colon) FFPE III Cetuximab
Candidate-Based PG Validation Studies(Secondary Analyses of Clinical Trials)
√
2012
2012
2011
2012
2012
RTOG9704 (Panc) 2013
FFPE III Gemcitabine
ICON7 2013 Blood III Bevacizumab
Study Name Approach Sample Size
Drug/Tx
Harvard-Toronto
Lung Cancer
Pathway
Candidate
3000+ Cisplatin
Carboplatin
Radiation
Harvard-Toronto
Pancreatic Cancer
Pathway
Candidate
GWAS
1000+ Gemcitabine
Harvard-Toronto
Esophageal Cancer
Pathway
Candidate
1000+ Cisplatin
5FU
Radiation
Toronto-Quebec Head and Neck Cancer*
Pathway
Candidate
GWAS
1400+ Radiation
Cisplatin
Candidate-Based PG Validation Studies(Secondary Analyses
of Observational Studies)
AMP-PEL Laboratory (Fall 2011)
Dr. Zhuo ChenDr. Dangxiao ChengDr. Azad KalamDr. Qi WangDr. Prakruthi PalepuDr. Salma MominDr. Ehab FadhelQin KuangKangping CuiMark MacPhersonAnna Sergiou
Devalben PatelMaryam MirshamsKevin BoydAlvina TseDr. Alex ChanDr. Wei XuDr. Manal NakhlaLawson EngAnthony LaDelfaMelody QiuMemori Otsuka
Dr. Marjan EmamiNicole PereraJennifer TeichmanBin SunAndrew FleetLorin DodbibaVincent PangDebbie JohnsonTammy PopperSharon FungDr. Olusola Faluyi
Steven HabbousHenrique HonJenny WangJenny HuiCrystal GagnonTeresa BiancoDr. Sinead CuffeAndrea P-CosioDr. Gord FehringerYonathan Brhane
Thank-you