< Main | May 22-23, 2007: Second Multi-IC Symposium on the Application of Genomic Technologies to Population-Based Studies: Facilitating Collaboration in Genome-Wide Association Studies
Background Materials
May 22, 2007 (2:00 - 5:30 p.m.)
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Study design: initial and replication studies, power:
Hoover RN. The evolution of epidemiologic research: from cottage industry to "big" science. Epidemiology. 2007 Jan;18(1):13-7  .
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. 2007 Jun;18(5):479-84 .
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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. 2006 Jun;38(6):663-7 .
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. 2007 May; 447: 161-5 .
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Challenges in analysis: computing platforms, spurious associations:
Ioannidis JPA (2005) Why most published research findings are false. PLoS Med 2(8): e124 .
Djulbegovic B, Hozo I (2007) When should potentially false research findings be considered acceptable? PLoS Med 4(2): e26. doi:10.1371/journal.pmed.0040026 .
Moonesinghe R, Khoury MJ, Janssens ACJW (2007) Most published research findings are false—But a little replication goes a long way. PLoS Med 4(2): e28. doi:10.1371/journal.pmed.0040028 .
Zollner S, Pritchard JK Overcoming the Winner’s Curse: Estimating Penetrance Parameters from Case-Control Data. AJHG 80:605-615, 2007 .
PLINK: http://pngu.mgh.harvard.edu/~purcell/plink/
U. Mich CaTS Power Calculator: http://www.sph.umich.edu/csg/abecasis/CaTS/
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Data resources for GWA studies:
CGEMS Web site: http://cgems.cancer.gov
dbGaP Web site: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=gap
Genetic Power Calculator (Shaun Purcell): http://pngu.mgh.harvard.edu/~purcell/gpc/
Quanto power calculator (W. James Gaudermann): http://hydra.usc.edu/gxe/
BC/Gene and BC/SNPmax: http://www.bcplatforms.com/contents/gene/geneinside.htm
HelixTree: http://www.goldenhelix.com/helixtree_pbat.html
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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. 2007 Apr 26 .
Saxena R, Voight BF, Lyssenko V, et al. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels. Science. 2007 Apr 26 .
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. 2007 Apr 26 .
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May 23, 2007 (8:30 a.m. - 5:30 p.m.)
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Introduction, goals, progress on recommendations from Multi-IC
I:
Summary and Recommendations from Multi-IC I
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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 2007; 39:631-7 .
Haiman CA, Patterson N, Freedman ML, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genetics 2007; 39:638-44 .
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 2007; 39:645-649 .
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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. 2007 Apr 26 .
Scott LJ, Mohlke KL, Bonnycastle LL et al. A Genome-Wide Association Study of Type 2 Diabetes in Finns Detects Multiple Susceptibility Variants. Science. 2007 Apr 26; PMID: 17463248 .
Saxena R, Voight BF, Lyssenko V, et al. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels. Science. 2007 Apr 26; PMID: 17463246 .
Gudmundsson J, Sulem P, Manolescu A, et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nature Genetics 2007; 39:631-7 .
Haiman CA, Patterson N, Freedman ML, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genetics 2007; 39:638-44 .
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 2007; 39:645-649 .
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Follow-up studies:
GWA Sequencing Workshop Report
NIGMS Workshop on Systems Biology and Complex Diseases
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 .
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 .
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Data sharing:
NIH-supported repositories and Web sites (New 6/26/08)
Database Web sites (New 6/26/08)
Example of GAIN data summaries generated by NCBI (pending) (New, 5/21/07)
Example of GEI data summary submitted by applicants (pending) (New 5/21/07)
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Consent/approvals:
Facilitating Collaboration with Informed Consent and IRB Approval: Lessons from The Candidate-gene Association Resource (CARE)
National Cell Repository for Alzheimer’s Disease (NCRAD): Consent Help Form
2007 Sample Consent form for Alzheimer’s Disease Genetics Research
CDC Genomics and Disease Prevention: Informed Consent Template for Population-Based Research Involving Genetics
Model consents from other studies
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Last Updated: August 5, 2008
Contact mcneilli@mail.nih.gov with any questions.
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