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Network of Networks, Cambridge UK
6 Octobre 2005
GENOMOS
“Genetic Markers for Osteoporosis”
RSC: Ioannidis, Ralston, Uitterlinden
EU FP5 sponsored
3 mio euro
QLK6-CT-2002-02629
Jan 2003 - Jan 2007
Osteoporosis is a genetic disease
•Classical genetic studies:
- FAMILIAL CLUSTERING: no Mendelian segregation patterns
- TWIN STUDIES: DNA similarity ~ bone similarity
•Human Genome Project: 15-20 million DNA polymorphisms
- DNA = Blue-print of life
- There is no “wild-type”: Each human has a unique genome
>> Genome variation causes bone variation
Dissection of a Complex Disease/Trait :
identify “risk” alleles of susceptibility genes
Type of approach
Resolution
“Top-down”/hypothesis free
* Whole-Genome-Linkage analysis
5-20 million bp
- Pedigrees
- Sib-pairs
- Human, mouse
* Whole-Genome-Association analysis
5-50 thousand bp
Effectiveness
+/?
- 100K – 1000K SNP analysis in cases/controls
“Bottom-up”/up-front hypothesis
* Association analyses of candidate
1 bp
+/-
gene polymorphisms (based on biology)
>>All approaches converge to testing (candidate) gene polymorphisms !
Molecular Genetic Epidemiology
Genome-wide association analysis
Specific Expression
Animal Model
Mendelian Disease
Identification of Candidate Gene
Identify DNA polymorphisms
Identify haplotypes
Association analysis
with disease phenotype in
populations
Functional analysis
in cells/serum/etc.
Meta-analysis to quantify effect size
IGFI, IGFBP3
GR, 11B-HSD
Cortisol
VDR,DBP
TSHR, DIO1, DIO2, DIO3, MCT8
Thyroid Hormone
Vitamin D
IGF/GH
ERα, ERβ, Aromatase,
LH, LHR, GnRH
Estrogen
Genetic determinants of osteoporosis ?
TGFb/BMP/Wntsignalling
TGFb, LRP5/6,
BMP2, FRZB,
SOST
homocysteine
Matrix molecules
Collagen Ia1, osteocalcin,
AHSG, LOX
MTHFR, MS, MTRR,
CBS, THYMS
Candidate gene association analysis “in practice”:
Many controversial & ir-reproducible results because of:
- Small sample size
- Ill-defined choice of polymorphisms
- Lack of standardized genotyping
- Lack of standardized phenotype data
- Publication bias
>> How to improve?
- Combine study populations across Europe: meta-analysis
- Rationalise choice of polymorphisms (functionality, haplotypes)
- Standardize genotyping methods: e.g., reference plate
- Standardize phenotypes across populations: meta-analysis
- Run prospective meta-analyses
GENOMOS (per january 2003)
a large-scale multicentre study for prospective meta-analyses of
osteoporosis candidate gene variants
“Genetic Markers for Osteoporosis”
EU FP5 sponsored
2
Aberdeen
3 mio euro
Aarhus
Total number of
subjects: 18.917
3
Jan 2003 – Jan 2007
Cambridge
5
6
“Maiden” publication:
7
Oxford
1
Rotterdam
14.622 women
Antwerp
ESR1, JAMA Nov 3, 2004:
4.295 men
Ioannidis et al.
4
4.952 fractures
Firenze
1.072 vertebral fx
9
Barcelona
8
Ioannina
9
= Participant + Epidemiological Cohort
7
= Participant
STRUCTURE OF “GENOMOS” WORKPLAN
WP 1
GENOTYPING
WP 2
FAMILY DATA
WP 3
HAPLOTYPING
WP 4
MONOGENIC GENES
WP 5
DNA POOLING
DATA GENERATION
GENOTYPE DATA OF POPULATIONS
META-ANALYSES
DATA ANALYSIS
WP6: ASSOCIATION WITH
FRACTURE, BMD, BONE LOSS
DELIVERABLES
DISSEMINATION,
COMMERCIALISATION
OSTEOPOROSIS
SUSCEPTIBILITYALLELES
WP 7: GENE
ENVIRONMENT
WP 8: GENE
ENVIRONMENT
INTERACTIONS:
INTERACTIONS:
Gene-nutrient interaction
Response-to-Treatment
DIETARY
TREATMENT
MODIFICATION
MODIFICATION
STRUCTURE OF “GENOMOS” MANAGEMENT
European Commission
Scientific Officer: Dr Christian Wimmer
COORDINATOR
participant 1 (Uitterlinden)
ADVISORY BOARD
Briggs (ESDN)
Kaufman (NEMO)
Levi (GENOSPORA)
Ralston (ANABONOS)
RESEARCH STEERING
COMMITTEE
WP 1
GENOTYPING
POPULATIONS
coordinator
participant 1 (Uitterlinden)
participant 1 (Uitterlinden)
participant 2 (Ralston)
participant 8 (Ioannidis)
WP 7
GENE-NUTRIENT
INTERACTION (Ca++)
coordinator
participant 5 (Reeve)
WP 2
GENOTYPING
FAMILIES
coordinator
participant 6 (Carey)
WP 3
HAPLOTYPING
coordinator
participant 1 (Uitterlinden)
WP 8
RESPONSE TO
HRT-TREATMENT
INTERACTION
coordinator
participant 3 (Langdahl)
WP 4
MONOGENIC
GENES
coordinator
participant 7 (van Hul)
WP 5
DNA POOLING
coordinator
participant 2 (Ralston)
WP 6
META-ANALYSES
coordinator
participant 8 (Ioannidis)
Candidate gene association analyses in GENOMOS
Genotype polymorphisms with prior evidence:
“fixed” polymorphisms
- Then genotype other polymorphisms with some evidence:
“free” polymorphisms
GENE
Vitamin D Receptor
SYMBOL
LOCATION
POLYMORPHISM
RISK ALLELE
FREQUENCY
VDR
12q13
M1/M4 (FokI RFLP)
M1 (f) =0.36
GA (Cdx2)
A=0.22
3’UTR haplotype
haplotype 1=0.45
haplotype 2=0.40
haplotype 3=0.11
Estrogeen Receptor-
Transforming Growth
Factor 1
Collagen Type I1
ESR1
TGF1
COLIA1
6q25
19q13
17q21
ex1-1146 (TA)n VNTR,
(TA)S=0.53
PvuII RFLP
P=0.46; p=0.54
XbaI RFLP
X=0.34; x=0.66
GA –800,
A=0.08
CT –509
T=0.36
Leu10Pro,
Pro=0.40
Arg25Pro,
Pro=0.07
Thr263Ile
Ile=0.04
GT intron 1 (Sp1)
T=0.18
total: 14 polymorphisms
SIZE MATTERS !!
“GENOMOS” (per may 2005)
a large-scale, multi-centre study for prospective meta-analyses of osteoporosis
candidate gene variants
“Genetic Markers for Osteoporosis”
Total number
of subjects:
26,264
EU FP5 sponsored: 3 mio euro
Jan 2003 – Jan 2007
Genes analysed:
- ESR1 (JAMA Nov 3, 2004: Ioannidis et al.)
- COLIA1 (manuscript subm)
- VDR (manuscript subm)
- TGFb (ongoing)
- LRP5&6 (ongoing)
18,405 women
2
16
Aberdeen
13
7,859 men
14
Aarhus
15
3
Cambridge
12 Amsterdam
1
Rotterdam* 10
7
Antwerp
6,498 fractures
5
11
Warsaw
2,380 vertebral fx
Graz
4
9
Firenze
Barcelona
8
9
= Participant + Epidemiological Cohort
7
= Participant
Ioannina
*coordinating centre