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PrintSecond 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
Summary and Recommendations from June 5-6 2006 Symposium 
Progress on Recommendations (as of May 17, 2007)
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
GWA Sequencing Workshop Reports [genesandenvironment.nih.gov]
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 Repository [nhlbi.nih.gov] NIAAA Collaborative Study on the Genetics of Alcoholism (COGA) [zork.wustl.edu] NIAAA Collaborative Study on the Genetics of Alcoholism (COGA) [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] caBIG/CGEMS Data Portal [caintegrator] dbGaP Genotype and Phenotype [ncbi.nlm.nih.gov] NIA Genetics Initiative NIA Genetics of Alzheimer Disease Data Storage Site [niageneticsdata.org] NIDA Center for Genetic Studies [zork.wutl.edu] NIMH Center for Collaborative Genetic Studies on Mental Disorders [zork.wustl.edu] NINDS Human Genetic Resource Center [ccr.coriell.org] Example of GAIN data summaries generated by NCBI
GAIN Data Manifest Submitted by Applicant NCBI Initial Analysis of GAIN Data, May 2006 NCBI Initial Analysis of GAIN Data, June 2006 GAIN Submitted Data Report GAIN Submitted Data Report 
Example of GEI data summary submitted by applicants
Example of GEI Data Manifest Example of GEI Variable Summary 
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 Genetic Studies 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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