1. 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

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

3.  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

4. 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

5. Interaction of NAT2 and Active Cigarette Smoking in Breast Cancer Risk Study Year# of CasesSmoking Group SubgroupNAT2 ↑ risk group 1996304AllPostmenopSlow 1997466FormerAllRapid 1998498RecentPostmenopRapid 2000113--- None 2000177AllPostmenopRapid 2001149All Rapid 2002442Recent≤50 yrs.Slow

6. # of cases # of SNPs Tier 1 443 198,000 Tier 2 332 1800 “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.”

7. 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%

8. Power of genome wide screen as a function of the number of retained false positive 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.010.1110100100010000100000 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

9. 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

10.  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

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

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

13. 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 IGFBP3 -202 (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

14. 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: http://epi.grants.cancer.gov/BPC3 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: https://caintegrator.nci.nih.gov/cgems/ 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: http://epi.grants.cancer.gov/PanScan/

15. Results: Overall in BPC3 rs#1447295

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

17. 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

18. rs979200 rs1456310 rs1016343 rs6470494 rs13281615 rs16902124 rs10808555 rs6983267 rs7837328 rs1447295 rs7837688 129.0 M 127.6 M MYC rs10505476 CGEMS region 1 CGEMS region 2 CGEMS region 3 CGEMS region 4 CGEMS region 5 CGEMS region 6 CGEMS region 7 CGEMS region 8 rs132544738 rs6983561 rs7824074 8q24 Region Cancer Susceptibility

19. 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) Nondrinker1.001.001.00 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

20. Leadership Roles Leadership Shared ComplementaryStudy Conduct ApportionedAnalysis and Publication

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

22. BPC3 Organization Data PoolingPublications Steering Committee PopulationGenotypingStatistics Genetics

23. Publication Leadership Interlymph Consortium Publications 2005-2007 Number:17 Number of different 1 st authors:13 Number of different last authors:14

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

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