Last updated: February 05, 2014
Second Multi-IC Symposium on the Application of Genomic Technologies to Population-Based Studies: Facilitating Collaboration in Genome-Wide Association Studies
Second Multi-IC Symposium on the Application of Genomic Technologies to Population-Based Studies: Facilitating Collaboration in Genome-Wide Association Studies
May 22-23, 2007
Background Materials
May 22, 2007: 2:00 p.m. - 5:30 p.m.
Study design: Initial and Replication Studies, Power
Hoover RN. The evolution of epidemiologic research: from cottage industry to "big" science. Epidemiology, 18(5):479-84. 2007. [PubMed]
Hunter DJ, Thomas G, Hoover RN, Chanock SJ. Scanning the horizon: What is the future of genome-wide association studies in accelerating discoveries in cancer etiology and prevention? Cancer Causes Control, 18(5):479-84. 2007. [PubMed]
Technologic Issues in GWA and Follow-up Studies
Pe'er I, de Bakker PI, Maller J, et al. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet, 38(6):663-7. 2006. [PubMed]
The Human Genome Structural Variation Working Group. Completing the map of human genetic variation: A plan to identify and integrate normal structural variation into the human genome sequence. Nature, 447:161-5. 2007. [PubMed]
Challenges in analysis: computing platforms, spurious associations
Ioannidis JPA. Why most published research findings are false. PLoS Med, 2(8): e124. 2005. [PubMed]
Djulbegovic B, Hozo I. When should potentially false research findings be considered acceptable? PLoS Med, 4(2):26. 2007. [PubMed]
Moonesinghe R, Khoury MJ, Janssens ACJW. Most published research findings are false-But a little replication goes a long way. PLoS Med, 4(2):e28. 2007. [PubMed]
Zollner S, Pritchard JK. Overcoming the Winner's Curse: Estimating Penetrance Parameters from Case-Control Data. AJHG 80:605-615, 2007. [PubMed]
PLINK: Whole genome association analysis toolset [pngu.mgh.harvard.edu]
University of Michigan CaTS Power Calculator [sph.umich.edu]
Data Resources for GWA Studies
Cancer Genetic Markers of Susceptibility (CGEMS) [cgems.cancer.gov]
db GaP Genotype and Phenotype [ncbi.nlm.nih.gov]
Genetic Power Calculator (Shaun Purcell) [pngu.mgh.harvard.edu]
Quanto Power Calculator (W. James Gaudermann) [hydra.usc.edu]
BC/Gene and BC/SNPmax [bcplatforms.com]
HelixTree Software [goldenhelix.com]
Dissemination/Publication: What to publish, when and how.
Scott LJ, Mohlke KL, Bonnycastle LL, et al. A Genome-Wide Association Study of Type 2 Diabetes in Finns Detects Multiple Susceptibility Variants. Science, 316(5829):1341-5. 2007. [PubMed]
Saxena R, Voight BF, Lyssenko V, et al. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels. Science, 316(5829):1331-6. 2007. [PubMed]
Zeggini E, Weedon MN, Lindgren CM, et al. Replication of Genome-Wide Association Signals in U.K. Samples Reveals Risk Loci for Type 2 Diabetes. Science, 316(5829):1336-41. 2007. [PubMed]
May 23, 2007: 8:30 a.m. - 5:30 p.m.
Introduction, goals, progress on recommendations from Multi-IC I
Summary and Recommendations from Multi-IC I
Replication Studies
Gudmundsson J, Sulem P, Manolescu A, et al. Genome-wide association study Identifies a second prostate cancer susceptibility variant at 8q24. Nature Genetics, 39:631-7, 2007. [PubMed]
Haiman CA, Patterson N, Freedman ML, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genetics, 39:638-44. 2007. [PubMed]
Yeager M, Orr N, Hayes RB, Jacobs KB, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nature Genetics, 39:645-649. 2007. [PubMed]
Cross-Study Analysis
Zeggini E, Weedon MN, Lindgren CM, et al. Replication of Genome-Wide Association Signals in U.K. Samples Reveals Risk Loci for Type 2 Diabetes. Science, 316(5829):1331-6. 2007. [PubMed]
Scott LJ, Mohlke KL, Bonnycastle LL, et al. A Genome-Wide Association Study of Type 2 Diabetes in Finns Detects Multiple Susceptibility Variants. Science, 316(5829):1341-5. 2007. [PubMed]
Saxena R, Voight BF, Lyssenko V, et al. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels. Science, 316(5829):1331-6. 2007. [PubMed]
Gudmundsson J, Sulem P, Manolescu A, et al. Genome-wide association study Identifies a second prostate cancer susceptibility variant at 8q24. Nature Genetics, 39:631-7. 2007. [PubMed]
Haiman CA, Patterson N, Freedman ML, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genetics, 39:638-44. 2007. [PubMed]
Yeager M, Orr N, Hayes RB, Jacobs KB, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nature Genetics, 39:645-649. 2007. [PubMed]
Follow-up studies
NIGMS Workshop on Systems Biology and Complex PhenotypesShu Y, et al. Effect of genetic variation in the organic cation transporter 1 (OCT1) on metformin action. Journal of Clinical Investigation, 117(5): 1422-31. 2008. [PubMed]
Reitman M and Schadt E. Pharmacogenetics of metformin response: a step in the path toward personalized medicine. Journal of Clinical Investigation, 117(5): 1226-29. 2007. [PubMed]
Data Sharing
NIH-Supported Repositories and Web Sites (Update 8/07/08)
- The National Cell Repository for Alzheimer's Disease (NCRAD)
- NIDDK Central Repository
- Type 1 Diabetes Genetics Consortium
- NHGRI Sample Repository for Human Genetic Research [ccr.coriell.org]
- NHLBI Biologic Specimen and Data Repository [nhlbi.nih.gov]
- NIAAA Collaborative Study on the Genetics of Alcoholism (COGA) [zork.wustl.edu]
- Collaborative Studies on the Genetics of Alcoholism (COGA) Study [niaaa.nih.gov]
- NIAID HIV/AIDS Specimen Repository [www3.niaid.nih.gov]
- NIDA Center for Genetic Studies [zork.wustl.edu]
- NIGMS Human Genetic Cell Repository [ccr.coriell.org]
Database Web Sites (Update 8/07/2008)
- T1DBase [t1dbase.org]
- dbGaP Genotype and Phenotype [ncbi.nlm.nih.gov]
- The Alzheimer's Disease Genetics Initiative [niageneticsinitiative.org]
- NIA Genetics of Alzheimer Disease Data Storage Site [niagads.org]
- NIDA Center for Genetic Studies [zork.wutl.edu]
- NIMH Center for Collaborative Genomics Studies on Mental Disorders [nimhgenetics.org]
- NINDS Human Genetic Resource Center [ccr.coriell.org]
Example of GAIN data summaries generated by NCBI
Example of GEI data summary submitted by applicants
Consent/Approvals
National Cell Repository for Alzheimer's Disease (NCRAD): Consent Help Form
2007 Sample Consent form for Alzheimer's Disease Genetics Research
Model Consents from Other Studies
Informed Consent Statement from NIDDK's Nonalcoholic Steatohepatitis Clinical Research Network
More information: The Clinical Research Network in Nonalcoholic Steatohepatitis (NASH)Pharmacogenetics Research Network Recommendations for Model Informed Consent Language, Terms, and Procedures from NIGMS Pharmacogenetics Research Network (PGRN)
More information: PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge BaseSample Consent Form from NIMH Human Genetics Initiative
More information: National Institute of Mental Health Center for Collaborative Genomics Research on Mental DisordersSample Informed Consent Language from NINDS Repository
More information: NINDS Human Genetics DNA and Cell Line RepositoryNHGRI's Medical Sequencing Program
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Last Updated: February 5, 2014