A Genome Wide Association Scan for Abdominal Aortic Aneurysm

1. A Genome Wide Association Scan for Abdominal Aortic Aneurysm Greg Jones Surgery Department, Otago Medical School New Zealand

2. Abdominal Aortic Aneurysm

4. AAA GWASPrimary Objectives 1) Perform whole genome analysis for AAA susceptibility. 2) Validation in separate AAA cohorts. 3) Establish a high-density whole genome elderly chronic disease free reference data set. 4) Determine specificity of AAA association by comparison with other vascular disease phenotypes.

5. AAA GWASDesign GWAS (Affymetrix SNP 6 Gene Chips) 625 cases versus 625 (AAA free) controls Validation in 4 separate cohort New Zealand, United Kingdom, Australia, Iceland >3,000 cases, 2,000-30,000 controls*

6. GWASDesign Issues 1. Case phenotype selection criteria 2. Control selection 3. Covariate analysis 4. Validation in independent cohorts 5. Complete replication of WGA studies 6. WGA statistical power

7. Design IssuesCase Phenotype Phenotype severity (AAA size) Pathogenic Heterogeneity Severity large aneurysms Stroke �heterogeneity of PathologySeverity large aneurysms Stroke �heterogeneity of Pathology

8. Design IssuesControl SelectionCovariate Analysis Age and Gender Matched Screened for AAA (aorta <25mm) Ethnicity Concurrent Vascular Disease Concurrent disease and CVD risk FactorsConcurrent disease and CVD risk Factors

9. Design IssuesValidation cohorts Cases and Matching Controls Second NZ cohort, Western Australia, Chichester and Leicester United Kingdom, Iceland/Netherlands Number of Markers to validate Expect <25% of GWAS SNPs to validate Number of markers high false positive rate. Select a suggestive threshold 10-5, clustering, common SNPs, gene associated markers to winnow list down.Number of markers high false positive rate. Select a suggestive threshold 10-5, clustering, common SNPs, gene associated markers to winnow list down.

10. Design IssuesGWAS replication NZ AAA GWAS (625 cases + 625 controls) Decode Genetics AAA (1400 cases + 30k �controls�) WTCCC AAA (2000 cases + 3000 �controls�) Genotyping Platform Genotyping platform Affy versus Illumina 370k, 500k, 1M CNV Genotyping platform Affy versus Illumina 370k, 500k, 1M CNV

11. Design IssuesStatistical Power Patterns of inheritance / expect effect sizes Staged design (Hirschhorn& Daly 2005) Stage 1. GWAS, liberal p-value for putative markers Stage 2. Re-test in independent secondary cohort, preferably another GWAS Stage 3. Validate small set of top hits other cohort Select a suggestive threshold 10-5, clustering, common SNPs, gene associated markers to winnow list down. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nature reviews. 2005;6(2):95-108 Select a suggestive threshold 10-5, clustering, common SNPs, gene associated markers to winnow list down. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nature reviews. 2005;6(2):95-108

12. GWAS IssuesAffymetrix SNP 6.0 DNA quality!!! Working within QC guidelines Affymetrix PCR work flow (48-96 samples) Budget for 15-20% extra consumables Genotyping console worklow(batch genotype call) Data management �BCSNPmax Plink &Haploview Affymetrix workflow Visual inspection of individual SNP plotsAffymetrix workflow Visual inspection of individual SNP plots