Second Multi-IC Symposium on the Application of Genomic Technologies to Population-Based 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 Phenotypes

Shu 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)

Database Web Sites (Update 8/07/2008)

Example of GAIN data summaries generated by NCBI

Example of GEI data summary submitted by applicants


Consent/Approvals

Facilitating Collaboration with Informed Consent and IRB Approval: Lessons from The Candidate-gene Association Resource (CARE)PDF file

National Cell Repository for Alzheimer's Disease (NCRAD): Consent Help FormPDF file

2007 Sample Consent form for Alzheimer's Disease Genetics ResearchPDF file

CDC Genomics and Disease Prevention: Informed Consent Template for Population-Based Research Involving GeneticsPDF file

Model Consents from Other Studies

Informed Consent Statement from NIDDK's Nonalcoholic Steatohepatitis Clinical Research Network PDF file
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) PDF file
More information: PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base

Sample Consent Form from NIMH Human Genetics Initiative PDF file
More information: National Institute of Mental Health Center for Collaborative Genomics Research on Mental Disorders

Sample Informed Consent Language from NINDS RepositoryPDF file
More information: NINDS Human Genetics DNA and Cell Line Repository

NHGRI's Medical Sequencing Program

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Last Updated: February 5, 2014