# Presentation: 074244

## Session 1

- Replication
- Replication
- Replication

## Session 1

- Stephen Chanock, NCI
- Cashell Jaquish, NHLBI
- Teri Manolio, NHGRI
- Winnifred Rossi, NIA

## Need for Consensus on What Constitutes Replication

**Avalanche of GWAS and candidate gene studies**
**Replication: *****sine qua non***
**Likelihood of single study establishing an association is low **_***until***_** studies are sufficiently powered. ****	**
**Sample sizes increase sufficiently **
**Analytical methods improve substantially**
**Common problem of how to interpret confusing and spurious findings**
**Multiple markers & study designs**

## Phylogenetic Tree of Five Common Haplotypes of DTNBP1

**Mutsuddi et al, *****Am J Hum Genet  *****2006; 79:903-909.**

- Possible Association with Schizophrenia

## “Positively” Associated Haplotypes Differ in All Six Studies

**Mutsuddi et al, *****Am J Hum Genet  *****2006; 79:903-909.**

- Each common DTNBP1 haplotype was tagged but multiple association signals observed. Strong possibility that more than one common variant contributes to schizophrenia risk at DTNBP1 locus

## Challenges in Replication Studies:aka...how not to do a study

**Use different phenotypes**
**Use  different markers**
**Mix fine-mapping and replication**
**Use different analytic methods (haplotype vs. single marker)**
**Fail to adequately account for differences in populations**
**Distinct populations**
**High heterogeneity within a study**

## Proposed Criteria for Positive Replication*

**Sufficient sample size in soundly designed study**
**Same gene**
**Same SNP (or SNP in complete LD with prior SNP, r****2**** = 1)**
**Comparable genetic model**
**Same direction as original finding**
**Highly significant association reporting**
**Initial Report**
**Joint or Combined Analysis Preferred**
**Same or very similar population**

****NCI-NHGRI Working Group on Criteria for Genotype-Phenotype Association***

- Chanock et al *Nature* in press

## How Do We Get to Replication?

## SNP Health Association Resource(SHARe)

- Genotyping of all consenting subjects from 3 generations (N~10,000) of the Framingham Heart Study
- 550K SNPs (Affymetrix) in each subject
- Plan to genotype two more cohorts
- Include all available phenotypes, clinical outcomes and genotypes in dbGAP
- Individual data will be shared openly for replication and gene finding

## Candidate Gene Association Resource (CARE)

- Create 50,000 person cohort with genotyping of 1,700+ candidate genes
- Complete 500k SNP genotyping on a subset of the combined cohorts
- Merge harmonized phenotype data for multiple studies with genotype data
- Openly shared data source
- Utilizes a more standardized consortium effort for replication

## SNP Typing for Association with Multiple Phenotypes from Existing Epidemiologic Data (STAMPEED) 

- Supports genome wide SNP typing and analysis in existing clinical trial, cohort, case-control or family studies.
- 13 R01s investigating heart, lung and blood phenotypes
- Close to 30,000 people will be genotyped
- Studies were required to have a plan in place for replication and validation
- Investigators initiated working groups within STAMPEED to replicate findings
- Investigator initiated collaborative approach to replication
- Investigators expressed a need for “rapid response” resource for replication and validation

## Genotype, Haplotype, Sequence

**Follow-up Study #1 **
**4600 cases/ 4600 controls**

**Follow-up Study #2**
**3500 cases/ 3500 controls**

**Fine Mapping**

**Initial Study**
**1150 cases/1150 controls**

**>28,000 SNPs**

*at least* **1,500**
**SNPs**

**30 ±20**
**loci**

**540,000 Tag SNPs**

**General Strategy for Prostate & Breast Cancer**
**GWAS**

*Genotype, Haplotype, Sequence*

***Determine Causal Variant(s)***

**Notes:**
Cone of Truth
Well powered to determine true positives 
Economic considerations included- ie too expensive still to scan all
We are in the midst of follow-up 1 for prostate and starting followup 1 for breast cancer scans

## Replication Studies in  CGEMS Prostate Cancer GWAS

**PLCO**

**ACS**

**ATBC**

**FPCC**

**HPFS**

**ALL**

**Subjects**

**1157**

**1172**

**Predisposing **
**allele frequency**

**0.55**

**0.49**

**1151**

**1150**

**0.55**

**0.50**

**896**

**894**

**0.57**

**0.51**

**459**

**455**

**0.56**

**0.51**

**636**

**625**

**0.57**

**0.51**

**4299**

**4296**

**0.56**

**0.50**

**P-value**

**2.4****x****10****-05**

**3.2****x****10****-03**

**1.9****x****10****-03**

**1.2****x****10****-01**

**1.0****x****10****-02**

**9.4****x****10****-13**

**Predisposing **
**allele frequency**

**0.14**

**0.10**

**0.12**

**0.08**

**0.21**

**0.17**

**0.12**

**0.07**

**0.13**

**0.09**

**0.15**

**0.11**

**P-value**

**9.8****x****10****-05**

**2.7****x****10****-05**

**2.9****x****10****-02**

**4.4****x****10****-03**

**2.7****x****10****-03**

**1.5****x****10****-14**

**rs6983267**

**rs1447295**

**Cases**

**Cont.**

**Cases**

**Cont.**

- Estimated Odds Ratios Overall
- Heterozygotes       	1.26			1.43
- Homozygotes  	1.58			 2.23

## Meta-Analysis of 8q24 papers in Nature Genetics: J Witte

*J Witte Nature Genetics 2007*

## Issues in Replication

- Built-in Replication vs “1000 Flowers Blooming”
- Public Health or Clinical Significance
- Population Genetics
- When is it Not Replication?
- Special Populations
- Barriers to Timely Conduct Follow-up
- Data Availability/Access
- Reporting of Negative Results
- Sufficient Detail for Inspection of Data

## Issues in Developing Consortia

- Why do we need consortia?
- When are they needed?
- What aspects of GWA studies should they address?
- How should they be developed?
- Who should participate?
- What are the incentives for collaboration?
- Publication?
- Data access?