GREG JONESGREG JONES

SURGERY DEPARTMENT, OTAGO SURGERY DEPARTMENT, OTAGO MEDICAL SCHOOLMEDICAL SCHOOL

NEW ZEALANDNEW ZEALAND

1)1) Perform whole genome analysis for AAA Perform whole genome analysis for AAA susceptibility. susceptibility.

2)2) Validation in separate AAA cohorts.Validation in separate AAA cohorts.

3)3) Establish a high-density whole genome Establish a high-density whole genome elderly chronic disease free reference data elderly chronic disease free reference data set. set.

4)4) Determine specificity of AAA association by Determine specificity of AAA association by comparison with other vascular disease comparison with other vascular disease phenotypes.phenotypes.

GWAS (Affymetrix SNP 6 Gene Chips)GWAS (Affymetrix SNP 6 Gene Chips)

625 cases versus 625 (AAA free) controls625 cases versus 625 (AAA free) controls

Validation in 4 separate cohortValidation in 4 separate cohort

New Zealand, United Kingdom, Australia, New Zealand, United Kingdom, Australia, IcelandIceland

>3,000 cases, 2,000-30,000 controls*>3,000 cases, 2,000-30,000 controls*

1. Case phenotype selection criteria 1. Case phenotype selection criteria

2. Control selection2. Control selection

3. Covariate analysis 3. Covariate analysis

4. Validation in independent cohorts 4. Validation in independent cohorts

5. Complete replication of WGA 5. Complete replication of WGA studiesstudies

6. WGA statistical power6. WGA statistical power

Phenotype severity (AAA size)Phenotype severity (AAA size)

Pathogenic HeterogeneityPathogenic Heterogeneity

Age and Gender MatchedAge and Gender Matched

Screened for AAA (aorta <25mm)Screened for AAA (aorta <25mm)

EthnicityEthnicity

Concurrent Vascular Disease Concurrent Vascular Disease

Cases and Matching ControlsCases and Matching Controls

Second NZ cohort, Western Australia, Second NZ cohort, Western Australia, Chichester and Leicester United Chichester and Leicester United Kingdom, Iceland/NetherlandsKingdom, Iceland/Netherlands

Number of Markers to validateNumber of Markers to validate

Expect <25% of GWAS SNPs to validateExpect <25% of GWAS SNPs to validate

NZ AAA GWASNZ AAA GWAS

(625 cases + 625 controls)(625 cases + 625 controls)

Decode Genetics AAADecode Genetics AAA(1400 cases + 30k ‘controls’)(1400 cases + 30k ‘controls’)

WTCCC AAAWTCCC AAA(2000 cases + 3000 ‘controls’)(2000 cases + 3000 ‘controls’)

Genotyping PlatformGenotyping Platform

Patterns of inheritance / expect effect Patterns of inheritance / expect effect sizessizes

Staged design Staged design (Hirschhorn& Daly 2005)(Hirschhorn& Daly 2005)

Stage 1. GWAS, liberal p-value for putative markersStage 1. GWAS, liberal p-value for putative markers

Stage 2. Re-test in independent secondary cohort, Stage 2. Re-test in independent secondary cohort, preferably another GWASpreferably another GWAS

Stage 3. Validate small set of top hits other cohortStage 3. Validate small set of top hits other cohort

1.1. DNA quality!!!DNA quality!!!

2.2. Working within QC guidelinesWorking within QC guidelines3.3. Affymetrix PCR work flow Affymetrix PCR work flow (48-96 samples)(48-96 samples)

4.4. Budget for 15-20% extra consumablesBudget for 15-20% extra consumables5.5. Genotyping console worklowGenotyping console worklow(batch genotype (batch genotype

call)call)

6.6. Data management Data management –BCSNPmax–BCSNPmax

7.7. Plink &HaploviewPlink &Haploview

Andre van RijAndre van RijVicky PhillipsVicky PhillipsGrace YuGrace YuOtago Vascular DiagnosticsOtago Vascular Diagnostics

Tony MerrimanTony MerrimanLes McNoeLes McNoe

The NZ Vascular Society The NZ Vascular Society Aneurysm ConsortiumAneurysm ConsortiumDavid Lewis (CDHB)David Lewis (CDHB)ThodurVasudevan (WDHB)ThodurVasudevan (WDHB)Ross Blair (WDHB)Ross Blair (WDHB)Andrew Hill (ADHB)Andrew Hill (ADHB)

Andre van RijAndre van RijVicky PhillipsVicky PhillipsGrace YuGrace YuOtago Vascular DiagnosticsOtago Vascular Diagnostics

Tony MerrimanTony MerrimanLes McNoeLes McNoe

The NZ Vascular Society The NZ Vascular Society Aneurysm ConsortiumAneurysm ConsortiumDavid Lewis (CDHB)David Lewis (CDHB)ThodurVasudevan (WDHB)ThodurVasudevan (WDHB)Ross Blair (WDHB)Ross Blair (WDHB)Andrew Hill (ADHB)Andrew Hill (ADHB)

Western Australian HIMS / AAA study Western Australian HIMS / AAA study Paul Norman (UWA)Paul Norman (UWA)

BHF Cardiovascular Genetics Lab (UCL)BHF Cardiovascular Genetics Lab (UCL)Steve HumphriesSteve HumphriesAndy ThompsonAndy Thompson

Jackie CooperJackie Cooper

The Aneurysm ConsortiumThe Aneurysm ConsortiumMatt Bown (St Georges)Matt Bown (St Georges)HanyHefez (Chichester)HanyHefez (Chichester)

Wellcome Trust Sanger InstituteWellcome Trust Sanger Institute

DeCodeGeneticsDeCodeGenetics

This work was supported by theThis work was supported by theHealth Research Council of New ZealandHealth Research Council of New Zealand