Homeright arrowAbout NHGRIright arrowOrganizational Structureright arrowAbout the Office of the Directorright arrowOffice of Population Genomicsright arrowOPG: Research Programsright arrowThe Genetic Association Information Network (GAIN) right arrowGain Analysis Workship II
Share this page

Gain Analysis Workshop II

Agenda and Presentations

October 17-18, 2007
Wednesday, October 17, 2007

All presentations are in PDF format
To view the PDF document(s) on this page, you will need Adobe Reader. Download Adobe Reader

7:00 - 8:30 a.m. Continental Breakfast and Registration  
8:30 - 8:45 a.m. Welcome: Introduction and Agenda Francis Collins
8:45 - 9:15 a.m. Overview: Status of GAIN
  • Data available, presentation/publication plans
  • GAIN 2.0
  • Mental health disorders collaboration

Teri Manolio
David Wholley
Patrick Sullivan
9:15 - 10:30 a.m. GAIN Genotyping
  • Broad genotyping center update
  • Review of genotyping QA pipeline
  • QA process and results to date


Stacey Gabriel
Finny Kuruvilla
Justin Paschall
10:30 a.m. Discussion  
10:45 - 11:15 a.m. Break  
11:15 - 11:45 a.m. GAIN Genotyping (continued)
  • Groups whose genotypes are completed describe their experience with working through
    QC issues

Ben Neale
James Warram
Patrick Sullivan
11:45 a.m. - Noon GAIN Datasets
  • Updating and versioning data releases beyond the initial one

James Ostell
12:00 - 12:30 p.m. Discussion  
12:30 - 1:30 p.m. Lunch  
  Afternoon Session  
1:30 - 2:30 p.m. Imputation
  • IMPUTE Method
  • MACH Method
  • TUNA Method
  • GAIN progress to date

Jonathan Marchini
Gonçalo Abecasis
Dan Nicolae
Itsik Pe'er
2:30 - 3:00 p.m. Bayes Factors
  • Meaning and use
  • Comparison to p-values in GAIN
 Jonathan Marchini
3:00 - 3:30 p.m. Discussion  
3:30 - 4:00 p.m. Break  
4:00 - 5:00 p.m. Assessing and analyzing copy number variants in GAIN platforms Steve McCarroll
5:00 - 5:45 p.m. Analysis of and adjustment for population structure Paul de Bakker
Gilles Thomas
5:45 - 6:00 p.m. Discussion  
6:00 p.m. Adjorn  
6:30 p.m. Reception  

Thursday, October 18, 2007
7:00 - 8:00 a.m. Continental Breakfast  
8:00 - 9:00 a.m. GAIN Data Access Experience and Ongoing Issues
  • Brief review of access process, status of distribution, use
  • GAIN human subjects protections: view from external review committees/IOM panel
  • NIH GWAS Policy
 Emily Harris
Wylie Burke
Laura Rodríguez
9:00 - 9:15 a.m. Discussion  
9:15 - 10:00 a.m. WTCCC Bipolar Disorder
  • Genotype QC filtering
  • Population structure
  • Initial GWA findings, replication
  • Cross-study analyses
  • Follow-up of initial findings
 Nick Craddock
10:00 - 10:15 a.m. Break  
10:15 - 11:00 a.m. FUSION Type II Diabetes
  • Genotype QC filtering
  • Population structure
  • Initial GWA findings, replication
  • Cross-study analyses, including CAD and obesity
  • Follow-up of initial findings
 Mike Boehnke
11:00 - 11:45 a.m. Prostate Cancer
  • Genotype QC filtering
  • Population structure
  • Initial GWA findings, replication
  • Cross-study analyses, including breast and colon cancer
  • Follow-up of initial findings
 Matthew Freedman
11:45 a.m. - 12:30 p.m. Breast Cancer
  • Genotype QC filtering
  • Population structure
  • Initial GWA findings, replication
  • Cross-study analyses
  • Follow-up of initial findings
 Steve Chanock
12:30 - 1:30 p.m. Lunch  
1:30 - 2:15 p.m. Crohn's Disease
  • Genotype QC filtering
  • Population structure
  • Initial GWA findings, replication
  • Cross-study analyses
  • Follow-up of initial findings
 Dan Nicolae
2:15 - 3:00 p.m Panel discussion (all five speakers) Moderator:
Francis Collins
3:00 - 3:30 p.m. Conclusion and next steps John Kelsoe
Teri Manolio
3:00 - 3:30 p.m. Adjournment Francis Collins

Top of page

Last Reviewed: July 27, 2009