Promoting Collaborations Across Studies for Replication and Follow-up Studies Robert N. Hoover, M.D., Sc.D Director Epidemiology and Biostatistics Program June 22, 2007

Outline MEETING THE REQUIREMENTS FOR GOOD SCIENCE Extent of Collaboration Leadership Roles Resource Enhancement Training Institutional Incentives

 Very large studies  Replication, replication, replication (planned and coordinated)  Rigorous, high-quality design, conduct, analysis –Genomics –Epidemiology –Statistics –Informatics  Data sharing  Accomplished Through Consortia GWAS: WHAT WORKS

Review of Genetic Association Studies 603 associations of polymorphisms and disease 166 studied in at least three populations Only six seen reproducibly (>75% of studies) Hirschhorn et al., Genetics in Medicine, 2002

Interaction of NAT2 and Active Cigarette Smoking in Breast Cancer Risk Study Year# of CasesSmoking Group SubgroupNAT2 ↑ risk group AllPostmenopSlow FormerAllRapid RecentPostmenopRapid None AllPostmenopRapid All Rapid Recent≤50 yrs.Slow

# of cases # of SNPs Tier ,000 Tier “We identified 11 SNPs that were associated with PD (P<.01) in both tier 1 and tier 2 samples and had the same direction of effect.” (Maraganore et al) “In this issue, four investigative teams …have sought to replicate the findings from a GWA study of PD by Maraganore et al. Taken together these four studies appear to provide substantial evidence that none of the SNPs originally featured as potential PD loci are convincingly replicated and that all may be false positives.”

Study Size to Detect a Two-Fold Interaction True prevalence of exposure No. of cases (=No. of controls) Prevalence of genotype=10% Exposure specificity=100% Exposure sensitivity = 100% Exposure sensitivity = 80% Exposure sensitivity = 60%

Power of genome wide screen as a function of the number of retained false positive Model : One susceptibility allele : MAF = 0.1, Odds Ratio = 1.4 LD of typed marker with susceptibility marker : r 2 = 0.8 Number of cases/control pairs : 1,200 Number of markers types : 500,000 Number of false positives Power

Lung Cancer Risk and CYP2D6* Study 1Study 2Study 3 Relative Risk15. 6 (4.8 – 55.9) 6.1 (2.2 – 17.1)0.6 (0.3 – 1.2) Epidemiologic Quality LowIntermediateHigh (% participation)(?)(26%)(80%) * Risk of homozygous extensive metabolizers compared to homozygous poor metabolizers. STUDY QUALITY

 Very large studies  Replication, replication, replication (planned and coordinated)  Rigorous, high-quality design, conduct, analysis –Genomics –Epidemiology –Statistics –Informatics  Data sharing  Accomplished Through Consortia GWAS: WHAT WORKS

MEETING THE REQUIREMENTS FOR GOOD SCIENCE Extent of Collaboration Leadership Roles Resource Enhancement Training Institutional Incentives

Breast Cancer Association Consortium Cases 20 studies: 28,000 cases 30,000 controls

Breast Cancer Association Consortium: Findings to Date 20 candidate SNPs (published + unpublished) Some evidence No association ADH1C I350V AURKA F31I XRCC1 R399Q LIG4 D501D BRCA2 N372H XRCC3 T241M XRCC3 5’UTR XRCC3 IVS5 XRCC2 R188H ERCC2 D312N TP53 R72P BCAC, JNCI (2006) 9 SNPs 11 SNPs Strong CASP8 D320H (P=1x10 -7 ) No association SOD2 V16A ADH1B 3’UTR CDK1A S31R ICAM5 V301I NUMA1 A794G Reasonable TGFB1 L10P (P=0.0001) (ER-, PR- tumors) Moderate IGFBP (p=0.05) ATM S49C (p=0.09) 9-15 studies: 10,783 cases, 18,312 controls Cox A/Dunning AM/Garcia-Closas M for the BCAC Nat Genet 2007;39:688 Follow-up

25+ cohorts, over 2.6 million individuals (1.2 million with DNA collected at baseline) CGEMSPanScanBPC3 Cohorts: ATBC, CPS II, EPIC, HPFS, MEC, NHS, PHS, PLCO, WHS Risk Factors: Hormone risk factors and hormones Genes: 53 in steroid hormone and growth factor pathways Cancer Sites: Breast & Prostate cancer Cases with DNA: Website: Scan: PLCO, NHS Replication: ATBC, CPS II, EPIC, HPFS, MEC, PHS, WHS, WHI Risk factors: Same as BPC3 plus family history Genes: Genome-wide Association Study (GWAS) Cancer Sites: Breast & Prostate cancer Cases with DNA: 8,850 breast cases, 6,160 prostate cases Data Portal: Scan: ATBC, CLUE II, CPS II, EPIC, HPFS, NHS, NYUWHS, PHS, PLCO, SMWHS, WHI, WHS Replication: Pancreatic Cancer Case-Control Consortium (PANC4) Risk Factors: Tobacco, obesity, family history and diabetes Genes: Genome-wide Association Study (GWAS) Cancer Sites: Pancreatic cancer Cases with DNA: ~1,900 pancreatic cases Website:

Results: Overall in BPC3 rs#

Extent of Collaboration Limited Replication or More –Main Effects –Fine Mapping –Gene X Gene –Gene X Environment –Candidate Pathways –Other Phenotypes and Outcomes

Flow of Investigation: From Genome- Wide Association to Clinical Translation Sequencing/Genotyping Functional Studies Translational Studies Initial Genome-Wide Association (GWA) Studies Replication/Fine Mapping Data Analysis Database

rs rs rs rs rs rs rs rs rs rs rs M M MYC rs CGEMS region 1 CGEMS region 2 CGEMS region 3 CGEMS region 4 CGEMS region 5 CGEMS region 6 CGEMS region 7 CGEMS region 8 rs rs rs q24 Region Cancer Susceptibility

Alcohol Consumption and NHL a Pooled InterLymph Analysis Risk of NHL subtypes associated with alcohol consumption CLL/SLL(N=814)Diffuse(N=1972)Follicular(N=1194) Alcohol exposure OR (95% CI) Nondrinker Ever drinker 0.90 (0.75, 1.09) 0.74 (0.66, 0.84) 0.83 (0.71, 0.95) Current Current 0.81 (0.59, 1.10) 0.63 (0.52, 0.76) 0.80 (0.64, 1.00) Former Former 1.05 (0.69, 1.60) 0.92 (0.72, 1.18) 0.94 (0.69, 1.27) Morton LM et al. – 2005 Lancet Oncology

Leadership Roles Leadership Shared ComplementaryStudy Conduct ApportionedAnalysis and Publication

InterLymph Organization Behavior and EnvironmentHost and Genetics Executive Committee Immunity and InfectionPathology and Survival

BPC3 Organization Data PoolingPublications Steering Committee PopulationGenotypingStatistics Genetics

Publication Leadership Interlymph Consortium Publications Number:17 Number of different 1 st authors:13 Number of different last authors:14

Resource Enhancement Infrastructure – extraction, additional specimens or data, biomarkers Additional Genotyping

Institutional Incentives Investigator’s Institution - Promotion/Tenure - Infrastructure Funding Institutions - Support for Consortia - Targeted funding opportunities - Base support for contributing studies