AllerGen / Vancouver - 01/03//2009 Meta-Analysis of GABRIEL GWAS Asthma & IgE F. Demenais, M....
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Transcript of AllerGen / Vancouver - 01/03//2009 Meta-Analysis of GABRIEL GWAS Asthma & IgE F. Demenais, M....
AllerGen / Vancouver - 01/03//2009
Meta-Analysis of GABRIEL GWASAsthma & IgE
F. Demenais, M. Farrall, D. StrachanGABRIEL Statistical Group
AllerGen / Vancouver - 01/03//2009
GABRIEL Phase I GWAS
GWAS (Illumina 300K) of UK & German data
→ 17q21 locus (ORMDL3) associated with asthma Moffat et al, Nature, 2007
Replication of this association by several studies
Genetic heterogeneity at 17q21 locus (French EGEA data) → Effect of 17q21 variants restricted to early-onset asthma and enhanced by early-life exposure to ETS Bouzigon et al, New Engl J Med, 2008
AllerGen / Vancouver - 01/03//2009
Aim of Phase II Gabriel GWAS
To identify associations of genetic variants with:
- susceptibility to asthma
(childhood onset, adult onset, industrial)
- total IgE levels
across populations of European ancestry using Illumina Human 610-Quad beadchip
by conducting a meta-analysis of all studies
AllerGen – Vancouver – 01/03/2009
DATA AVAILABLE for Phase II GWAS
- Most datasets are cases/controls
- A few datasets include families: MRC (UK), EGEA (French), Canadian, Russian, GSK…
Childhood onset Asthma 20 012 subjects
Adult onset Asthma
Industrial Asthma 1356 subjects
ALSPAC J . Henderson/W. McArdle 1292 1249BAMSE G. Pershagen 567 in progressB58C D. Strachan 911 904ECRHS D. J arvis/M. Wjst 2433 2370EGEA F. Demenais/F. Kaufmann 2034 2034FINRISK L. Vonhertzen 152 151GABRIEL AS E. von Mutius/M. Kabesch 1727 1710INDUS I. Wouters/D. Heederick 1356 1317MAS Y. Lee/I. Marenholz 184 183PIAMA D. Postma/G. Koppelman 423 406POLONIKOV A. Polonikov 682 634SAPALDIA N. Probst/M. Imboden 1640 1640SEVERE M. Moffatt/W. Cookson 366 362TOMSKA E. Bragina/M. Freidin 804 736UFA E. Khusnutdinova 727 715
BUSSELTON A. J ames 1598 1530CANADA - CAPPS & SAGE T. McDonald/D. Daley 1310 1109CANADA - SLSJ C. Laprise 1282 1268GSK-GAIN S. Pillai 1880 1844
TOTAL: 20729
POPULATION/COHORTContact Name/Principal
InvestigatorSamples selected
for Phase IIPassed QC
GWAS Phase II DATA
Genotyping at CNG (Y. Gut, M. Lathrop, Evry, France)
Using Illumina Human 610-Quad beadchip
Initial QC processing at CNG (S.Heath, CNG) • % genotype calls - by individuals (< 95%: individuals excluded) • Relationship analysis to confirm known & identify cryptic relationships • Sex checks based on X-chromosome SNPs • Principal components analysis to identify cryptic non-European ancestry
Phase II GWAS: Overall Strategy
Analysis study by study (M Farrall, Oxford)
From Phenotypic data (each group) & Genotypic Data (CNG)
Meta-analysis of all studies: Phase II + Phase I (imputation)Asthma (F Demenais, Paris) IgE (D Strachan, London)
childhood onset, adult onset, all controls & cases separatelyindustrial asthma
AllerGen – Vancouver – 01/03/2009
Phenotypes
Asthma :Cases : doctor-diagnosed asthma or self-reported
+ age onset of asthma
Controls: unaffecteds (not selected as « hypernormal »
and may include other forms of wheezing)
→ Childhood Onset / Adult Onset Asthma using a cutoff of 16yrs
Controls drawn at random for childhood onset/ adult onset cases
IgE (log10) IgE wadjusted on sex and age-at-measurement by study and by case-control status
AllerGen – Vancouver – 01/03/2009
Method used for Study by Study Analysis
Single SNP analysis based on logistic regression models (linear
regression for IgE) allowing for familial clustering using STATA
Different models considered:
- additive model (1df)
- additive and non-additive effects ( 2 x 1 df)
- genotype association model (2 df)
Population Stratification:
Eigenvectors from PCA included in regression model
PCA uses HapMap data + CNG data (European controls)
AllerGen – Vancouver – 01/03/2009
Population stratificationPCA on European controls from French National Genotyping Center
Heath et al, Eur J Hum Genet, 2008
AllerGen – Vancouver – 01/03/2009
Meta-Analysis for Asthma & IgE
From the study-by-study analysis, tables generated including for each SNP:
QC metrics (MAF, SNP Call Rate, HW..) Number of cases / controls by genotype Regression coefficients & Standard errors Various test statistics
QC Filtering based on MAF (1% or 5%), SNP Call Rate (≥ 97%) HW (p > 10-4)
Meta-analysis using different methods
AllerGen – Vancouver – 01/03/2009
Methods used for Primary Meta-Analysis
• Fixed-effect (inverse variance weighted) models assumes that observed effects are estimates of a single effect average effect computed by weighting each study’s log OR
according to the inverse of their sampling variance
→ Test of homogeneity for SNP effect across studies using Cochran Q test
• Random-effect models (DerSimonian & Laird, 1986)
allows for effects to vary across studies
variance = between study variation + intra-study variation
preferred if # of study-specific estimates ≥ 5
AllerGen / Vancouver - 01/03//2009
Fixed vs Random effect Models
Example: Type 2 Diabetes (Ionnadis et al, PLoS one, 2007)
Meta-analysis of FUSION, DGI, WTCC
Gene SNP Q (p) I2 (95% CI) Random p Fixed p
rs9300039 0.019 75% (0-90) 0.015 4.3x10-7
FTO rs8050136 0.013 77% (0-91) 0.015 1.3x10-12
CDKAL1 rs10946398 0.16 46% (0-84) 3.2x10-6 4.1x10-11
PPARG rs1801282 0.15 47% (0-84) 0.0003 1.7x10-6
CDKN2B rs564398 0.48 0% (0-73) 1.2x10-7 1.2x10-7
HHEX rs5015480 0.45 0% (0-73) 5.7x10-10 5.7x10-10
AllerGen / Vancouver - 01/03//2009
Other Methods of Meta-analysis: Meta-Regression Bag & Nikolopoulos, Stat Appl Mol Biol, 2007
Study
i = 1, 2..k
Cases
yij = 1
Controls
yij =0
Genotype
j =1,2,..r
1 38 72 1
1 52 78 2
1 6 22 3
2 44 38 1
2 27 45 2
2 11 17 3
Logit (pij) = i + 2zi2 + 3zi3 if genotype effect cst between studies
Logit (pij) = i + 2zi2 + 3zi3 + i2 izi2 + i3 izi3 if gentoypexstudy int
→ Test for heterogeneity between studies using Multivariate Wald test
Possible to include random effect + various covariates
AllerGen / Vancouver - 01/03//2009
Other Approaches of Meta-Analysis
● Combining p-values or Z scores
● Local Score method (Guedj et al, 2006; Aschard et al, 2007) can detect aggregation of association signals
flexible approach which can use any test statistic
COHORT/POPULATION STATUS
ECRHS Data released to Martin FarrallEGEA Data released to Martin FarrallFINRISK Data released to Martin FarrallINDUS_1 Data released to Martin FarrallMAS Data released to Martin FarrallPIAMA Data released to Martin FarrallSAPALDIA Data released to Martin FarrallTOMSKA Data released to Martin FarrallUFA Data released to Martin Farrall
ALSPAC Awaiting data releaseB58C Awaiting data releaseGABRIEL AS Awaiting data releasePOLONIKOV Awaiting data releaseSEVERE Awaiting data release
GSK_GAIN Genotyping in progressINDUS_2 Genotyping in progressCANADA -SLSJ Genotyping scheduled Feb/MarCANADA -CAPPS & SAGE Genotyping scheduled Feb/MarBAMSE DNA QC in progressBUSSELTON DNA QC in progress
Outcome of Meta-Analysis
Identify Top SNPs (genome-wide significant)
Phase III Gabriel
Genotype top SNPs in 40 000 individuals
AllerGen / Vancouver - 01/03//2009
Gene-Gene Interactions
AllerGen / Vancouver - 01/03//2009
Various Methods to investigate GxG
- Regression-based methods (one stage, 2 stages…)
- Bayesian based approaches
- Data Reduction based-methods / Machine Learning
‘Combinatorial Partitioning Method (CPM), MDR)
- Pattern recognition models (neural networks)
- Combination of test statistics (meta-statistics)
Gabriel provides opportunity to compare these methods
by pooling data or in the context of meta-analysis
AllerGen / Vancouver - 01/03//2009
Gene-Environment Interactions
AllerGen / Vancouver - 01/03//2009
2 Step-Analysis to identify genes involved in GxEMurcray et al, Am J Epidemiol, 2008
Step 1: Screening test: case only analysis (combined case/control sample )
For each of N SNPs: LR Test for association between G and E
→ Select m SNPs with P < 1
Step 2 : Case- Control analysis
LR Test for GxE applied to m SNPs selected at step 1
→ Significance based on P < /m
Comparison with classical one-step approach applied to case-controls
→ Significance based on P < /N
AllerGen / Vancouver - 01/03//2009
Power for one-step and two-step analyses to detect GxE
for varying levels of interaction effect size
10,000 markers and 500 cases/500 controls
AllerGen / Vancouver - 01/03//2009
GABRIEL Working Groups
GW search for G X smoking in asthma M Boezen, D Postma, The Netherlands
Childood Asthma (M Kabesch) & Adult Asthma (D. Jarvis) to summarize data available in each study (phenotypes, environment)
Main areas of interest for collaborations: Phenotypes Environmental exposures : GxE Pathways: GxG Other types of variation: CNVs
Methodological issues
New opportunities that are going to emerge from the
AllerGen meeting