Pharmacogenetics in the treatment of breast and ovarian cancer patients

Peter A. Fasching

UCLUCLAA

David Geffen School of Medicine

Div. Hem/Onc

Concepts of science

Therapy A Therapy B

Therapy A must be better2

Pitfalls with this approach

Will this patient have a recurrence?

Therapie A

A: Therapy helped, and the patient has no recurrence.

B: Patient would not have gotten a recurrence anyway

3

Aim

A priori identification of patients with a benefit from the offered therapy

Test

Therapy will improve outcome Therapy will NOT

improve outcome

4

Gene expressionsFrom stromal cells

Gene expression profiles

SNP Chips (Germline-DNA)

Gene expression Profiling (WBC)

Epigenetic Profiling(circulating nucleic acids)

Gene copy variations

EpigenticProfiling

MutationProfiling

Proteomics

Biomaterials that could be helpful

miRNA Profiling

5

miRNAProfiling

SNP Chips (Germline-DNA)

Biomaterials that could be helpful

6

Can predict:

-Efficacy-Toxicity

Can discover:-functional explanation of differential response to chemotherapy

Tamoxifen

4-Hydroxy-Tamoxifen

N-Desmethyl-Tamoxifen

Endoxifen (N-Desmethyl-4-Hydroxy-Tamoxifen)

CYP3A4CYP3A5CYP2D6CYP2C9

CYP2C19CYP1A2

CYP2D6CYP3A4CYP2C9

CYP2C19CYP2B6

CYP2D6CYP2C9

CYP2C19CYP2B6

CYP3A4

Tamoxifen-Metabolism

7

CYP2D6 Genotyping as a predictive marker (Schroth, Goetz, Hamann, Fasching et al. JAMA 2009)

N=1325 ER positive Breast Cancer Patients

All treated with Tamoxifen

Genotyping CYP2D6

*3, *4, *5, *10, *41

Metabolizing Groups EM=extensive Metabolizers

IM=Intermediate Metabolizers

PM=Poor Metabolizers

8

The genome

wide approach

How many Single nucleodide Polymorphisms are out there?

About 3.3 Billion base pairsabout 24,000 genes

Persons genotyped

SNPs Polymorphic

1(20) + 2 or so ??? ???

240 10,000,000 3,100,000

1000 >15,000,000 >????

2001

2006

2009/2010

How many Single nucleodide Polymorphisms are out there?

Image Source: The Sanger Institute

>1,000,000 SNPs to be analyzed by chip technology on one chip

How to analyze and present 1,000,000 associations between genetic variations and the phenotype?

SNP1 (Chr1)

Genotype 1 Genotype 2

Phenotype 1 10% 50%

Phenotype 2 90% 50%

SNP2 (Chr1)

Genotype 1 Genotype 2

Phenotype 1 10% 10%

Phenotype 2 90% 90%

SNP3 (Chr1)

Genotype 1 Genotype 2

Phenotype 1 10% 20%

Phenotype 2 90% 80%

P=0,0000001

P=0,9

P=0,001

How can I present a million associations?

P=1

P=0,1

P=0,0001

P=0,001

P=0,01

P=0,00001

-lo

g1

0(p

-va

lue)

Conditional Logistic Regression Analyses*

Ingle et al. San Antonio 2010Chromosome Position

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 23

How to do the work? Clinical collaborators with well designed studies(!!!)

Biosampling infrastructure Genotyping Facility Biostatistics/Bioinformatics Functional Explanation

Clinical collaborators for clinical validation

R

E

C

DcTDcTDcT

SUCCESS A Study: Simultaneous Study of Gemcitabine-Docetaxel Combination adjuvant treatment Surveillance-Trial (n=3725) (PI: Prof. Dr. W. Janni)

DcT

E C

=Docetaxel

=Epirubicin =Cyclophosphamide

F

E

C

F

E

C

F

E

C

DcTDcTDcTF

E

C

F

E

C

F

G G G

G =GemcitabineF = 5-Flourouracil

Primary Objective

Disease free Survival

Secondary Objectives

Overall Survival, Toxicity, Quality of Life

R

Zoledronate2 years

Zoledronate5 years

21

Pre-planned Pharmacogenetic subprotocol

3602 out of 3754 patients (96%) provided DNA Samples (just one blood tube!!)

Collaborative application of Mayo Clinics (PI Dr. Weinshilboum) and SUCCESS Study Group (Co-PI Dr. Fasching) for NIH funding

NHGRI HG01 granted as part of a funding program for genome wide association studies for randomized trials

Structures for this collaboration

Blood ProcessingBlood ProcessingDNA ExtractionDNA ExtractionDNA NormalizationDNA NormalizationDNA PlatingDNA Plating

Data ManagementData ManagementData entryData entryData MonitoringData MonitoringData updatesData updates

GenotypingGenotypingPlate Map DesignPlate Map DesignGenotype Quality ControlGenotype Quality ControlDNA StorageDNA Storage

BiostatisticsBiostatisticsPhenotype Quality ControlPhenotype Quality ControlGx and Phx Data CleaningGx and Phx Data CleaningProvision of AnalysisProvision of Analysis

DNA AnalysisDNA AnalysisSNP Chip ProcessingSNP Chip Processing

CoordinationCoordinationCollboration with other GroupsCollboration with other GroupsWorking groups onWorking groups on•Phenotype HarmonizationPhenotype Harmonization•Genotype HarmonizationGenotype Harmonization•Statistical MethologyStatistical Methology•Ethical ConsiderationsEthical Considerations•Cross ValidationCross Validation•Further Clinical ValidationFurther Clinical Validation

Clinical CollaboratorsSUCCESS A

Study(GeparQuinto

Study)

Mayo Collaborators PGRN

BiostatisticsMolecular

PharmacologyHematology /

OncologyGenotype Core Facility

Cell Line ProgramCell Line ProgramHuman Variation PanelHuman Variation PanelBC Panel (UCLA)BC Panel (UCLA)

NIHNHGRI

GARNET (www.garnetstudy.org

)

Structures for this collaboration

Blood ProcessingBlood ProcessingDNA ExtractionDNA ExtractionDNA NormalizationDNA NormalizationDNA PlatingDNA Plating

Data ManagementData ManagementData entryData entryData MonitoringData MonitoringData updatesData updates

GenotypingGenotypingPlate Map DesignPlate Map DesignGenotype Quality ControlGenotype Quality ControlDNA StorageDNA Storage

BiostatisticsBiostatisticsPhenotype Quality ControlPhenotype Quality ControlGx and Px Data CleaningGx and Px Data CleaningProvision of AnalysisProvision of Analysis

DNA AnalysisDNA AnalysisSNP Chip ProcessingSNP Chip Processing

CoordinationCoordinationCollboration with other GroupsCollboration with other GroupsWorking groups onWorking groups on•Phenotype HarmonizationPhenotype Harmonization•Genotype HarmonizationGenotype Harmonization•Statistical MethologyStatistical Methology•Ethical ConsiderationsEthical Considerations•Cross ValidationCross Validation•Further Clinical ValidationFurther Clinical Validation

Clinical CollaboratorsSUCCESS A

Study(GeparQuinto

Study)

Mayo CollaboratorsBiostatistics

Molecular PharmacologyHematology /

OncologyGenotype Core Facility

Cell Line ProgramCell Line ProgramHuman Variation PanelHuman Variation PanelBC Panel (UCLA)BC Panel (UCLA)

NIHNHGRI

GARNET (www.garnet.org)

Genome-wide SNPs: Affy 6.0 and Illumina 550S and 510S. 1.3 million SNPs

Expression array: Affy U133 Plus2.0, 54,000 probe sets

Exon array

microRNA

CNV data

In-depth gene resequencing data

Mayo PGRN - “Human Variation Panel” Cell LinesUCLA – Human Individual Breast Cancer Cell Lines

MAYO - 300 lymphoblastoid Cell lines (Dr Wang)

UCLA - 52 Breast Cancer Cell lines (Dr Finn)

Genome-wide SNPs: Illumina 610K

Expression array: Agilent Human 44k

CNV Data

25

Where do we stand with Ovarian Cancer?The Ovarian Cancer Association Consortium

Coordinating Coordinating CentersCenters

Duke University, USA,Duke University, USA,USC (L.A.), USAUSC (L.A.), USACambridge, UKCambridge, UK

8 US 8 US SitesSites

4 Australian 4 Australian SitesSites

1 Asian 1 Asian SiteSite

12 European 12 European SitesSites

1 South American 1 South American SiteSite

1 African 1 African SiteSite

•26,000 Ovarian cancer patients with germline DNA26,000 Ovarian cancer patients with germline DNA•Epidemiological dataEpidemiological data•Clinical data, Therapy dataClinical data, Therapy data•Follow Up dataFollow Up data•Tissue Microarray with >9,000 SamplesTissue Microarray with >9,000 Samples

•31,000 Healthy Controls31,000 Healthy Controls•Epidemiological DataEpidemiological Data

Call for Data and sample pooling for drug/genotype Interactions

Behaviour

Primary Site

Sub Type

Stage

Histopathological grade

Miliary Disase

Residual Disease

First Line Chemotherapy Duration Chemotherapy Dose Chemotherapy

Progression (RECIST OR GCIG)

Death

Site Country Cases ChemoAOCS Australia 600 Platinum/taxane

MALOVA Denmark 680 Mostly pre-taxanes

LOS ANGELES USA 360 Platinum/taxane

MAYO USA 466 Platinum/taxane

BAVARIA Germany 271 Platinum/taxane

LEUVEN Belgium 296 Platinum/taxane

RPC 235 Platinum/taxane

YALE USA 96 Platinum/taxane

PVD 203 Platinum/taxane

SCOTROC1 GB 950 Platinum/taxane

GOG USA 493 Platinum/taxane

TOTAL 3970 Platinum/taxane

Work in Progress: Sets for analysis of PFS and Genotype

What would be future questions

Dramatically increase sample size for genomewide studies

Important Questions within randomized clinical trials