Pharmacogenetics in the treatment of
breast and ovarian cancer patients
Peter A. Fasching
David Geffen School of Medicine
Div. Hem/Onc
UCLA
Concepts of science
Therapy A
Therapy B
Therapy A must be better
2
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
Biomaterials that could be helpful
Gene expressions
From stromal cells
SNP Chips
(Germline-DNA)
Gene copy variations
Gene expression
profiles
Epigentic
Profiling
miRNA
Profiling
Mutation
Profiling
Gene expression
Profiling (WBC)
Epigenetic Profiling
(circulating nucleic acids)
miRNA
Profiling
Proteomics
5
Biomaterials that could be helpful
SNP Chips
(Germline-DNA)
Can predict:
-Efficacy
-Toxicity
Can discover:
-functional explanation of
differential response to
chemotherapy
6
Tamoxifen-Metabolism
Tamoxifen
CYP3A4
CYP3A5
CYP2D6
CYP2C9
CYP2C19
CYP1A2
CYP2D6
CYP3A4
CYP2C9
CYP2C19
CYP2B6
N-DesmethylTamoxifen
CYP2D6
CYP2C9
CYP2C19
CYP2B6
4-HydroxyTamoxifen
CYP3A4
Endoxifen
(N-Desmethyl-4Hydroxy-Tamoxifen)
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 pairs
about 24,000 genes
How many Single nucleodide Polymorphisms
are out there?
2001
2006
2009/
2010
Persons
genotyped
SNPs
Polymorphic
1(20) + 2 or so
???
???
240
10,000,000
3,100,000
1000
>15,000,000
>????
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%
P=0,0000001
SNP2 (Chr1)
Genotype 1 Genotype 2
Phenotype 1
10%
10%
Phenotype 2
90%
90%
P=0,9
SNP3 (Chr1)
Genotype 1 Genotype 2
Phenotype 1
10%
20%
Phenotype 2
90%
80%
P=0,001
How can I present a million associations?
P=0,00001
P=0,0001
P=0,001
P=0,01
P=0,1
P=1
-log10(p-value)
Conditional Logistic Regression Analyses*
1
2
3
4
5
6
7
8
9
10
11
Chromosome Position
Ingle et al. San Antonio 2010
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
SUCCESS A Study: Simultaneous Study of
Gemcitabine-Docetaxel Combination adjuvant
treatment Surveillance-Trial (n=3725) (PI: Prof. Dr. W. Janni)
F
F
E
E
F DcT DcT DcT
E
C
C
C
Zoledronate
2 years
R
R
F
F
E
E
C
C
F DcT DcT DcT
E
G G G
C
Zoledronate
5 years
Primary Objective
Disease free Survival
E =Epirubicin
C
=Cyclophosphamide
DcT =Docetaxel
F
= 5-Flourouracil
G
Secondary Objectives
=Gemcitabine
Overall Survival, Toxicity,
Quality of Life
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
Clinical Collaborators
SUCCESS A Study
(GeparQuinto Study)
Mayo Collaborators PGRN
Biostatistics
Molecular Pharmacology
Hematology / Oncology
Genotype Core Facility
Blood Processing
DNA Extraction
DNA Normalization
DNA Plating
Genotyping
Plate Map Design
Genotype Quality Control
DNA Storage
Data Management
Data entry
Data Monitoring
Data updates
Biostatistics
Phenotype Quality Control
Gx and Phx Data Cleaning
Provision of Analysis
Cell Line Program
Human Variation Panel
BC Panel (UCLA)
NIH
NHGRI
GARNET
(www.garnetstudy.org)
DNA Analysis
SNP Chip Processing
Coordination
Collboration with other Groups
Working groups on
•Phenotype Harmonization
•Genotype Harmonization
•Statistical Methology
•Ethical Considerations
•Cross Validation
•Further Clinical Validation
Structures for this collaboration
Clinical Collaborators
SUCCESS A Study
(GeparQuinto Study)
Mayo Collaborators
Biostatistics
Molecular Pharmacology
Hematology / Oncology
Genotype Core Facility
Blood Processing
DNA Extraction
DNA Normalization
DNA Plating
Genotyping
Plate Map Design
Genotype Quality Control
DNA Storage
Data Management
Data entry
Data Monitoring
Data updates
Biostatistics
Phenotype Quality Control
Gx and Px Data Cleaning
Provision of Analysis
Cell Line Program
Human Variation Panel
BC Panel (UCLA)
NIH
NHGRI
GARNET
(www.garnet.org)
DNA Analysis
SNP Chip Processing
Coordination
Collboration with other Groups
Working groups on
•Phenotype Harmonization
•Genotype Harmonization
•Statistical Methology
•Ethical Considerations
•Cross Validation
•Further Clinical Validation
Mayo PGRN - “Human Variation Panel” Cell Lines
UCLA – 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

Genome-wide SNPs: Affy 6.0 and Illumina 550S
and 510S. 1.3 million SNPs

Expression array: Agilent
Human 44k

Expression array: Affy U133 Plus2.0, 54,000
probe sets

CNV Data




Exon array
microRNA
CNV data
In-depth gene resequencing data
25
Where do we stand with Ovarian Cancer?
The Ovarian Cancer Association Consortium
8 US
Sites
12 European
Sites
Coordinating
Centers
1 Asian
Site
•26,000 Ovarian cancer patients with germline DNA
•Epidemiological data
•Clinical data, Therapy data
•Follow Up data
•Tissue Microarray with >9,000 Samples
1 South American
Site
Duke University, USA,
USC (L.A.), USA
Cambridge, UK
4 Australian
Sites
1 African
Site
•31,000 Healthy Controls
•Epidemiological Data
Call for Data and sample pooling for
drug/genotype Interactions
 Behaviour
 Miliary Disase
 Primary Site
 Residual Disease
 Sub Type
 First Line Chemotherapy
 Stage
 Histopathological grade
 Duration Chemotherapy
 Dose Chemotherapy
 Progression
 Death
(RECIST OR GCIG)
Work in Progress: Sets for analysis of PFS
and Genotype
Site
Country
Cases
Chemo
AOCS
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
235
Platinum/taxane
96
Platinum/taxane
203
Platinum/taxane
RPC
YALE
USA
PVD
SCOTROC1
GB
950
Platinum/taxane
GOG
USA
493
Platinum/taxane
3970
Platinum/taxane
TOTAL
What would be future questions
 Dramatically increase sample size for genomewide
studies
 Important Questions within randomized clinical
trials