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Genome-Wide Association for the Rest of Us: Introduction and Goals

Genome-Wide Association for the Rest of Us: Introduction and Goals. National Human Genome Research Institute. U.S. Department of Health and Human Services National Institutes of Health National Human Genome Research Institute. National Institutes of Health.

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Genome-Wide Association for the Rest of Us: Introduction and Goals

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  1. Genome-Wide Association for the Rest of Us: Introduction and Goals National Human Genome Research Institute U.S. Department of Health and Human Services National Institutes of Health National Human Genome Research Institute National Institutes of Health Teri A. Manolio, M.D., Ph.D.Senior Advisor to the Director, NHGRI, for Population Genomics Director, Office of Population Genomics June 22, 2007 U.S. Department of Health and Human Services

  2. 2007: The Year of GWA Studies? Hokusai, K. The Great Wave

  3. 2007: The Year of GWA Studies? Hokusai, K. The Great Wave

  4. 2007: The Year of GWA Studies? Hokusai, K. The Great Wave 27May2007

  5. 2007: The Year of GWA Studies? Sciencexpress, 3May2007

  6. 2007: The Year of GWA Studies? Sciencexpress, 26Apr2007

  7. 2007: The Year of GWA Studies? Nature Genetics, 1Apr2007

  8. 2007: The Year of GWA Studies? 26Oct2006 19Oct2006 10Mar2005 Sciencexpress

  9. What is a GWA Study? • Method for interrogating all 10 million variable points across human genome • Variation inherited in groups, or blocks, so not all 10 million points have to be tested • Blocks are shorter (so need to test more points) the less closely people are related • Technology now allows studies in unrelated persons, assuming ~10,000 base pair lengths in common (300,000 - 500,000 markers)

  10. Genome-Wide Scan for Type 2 Diabetes in a Scandinavian Cohort http://www.broad.mit.edu/diabetes/scandinavs/type2.html

  11. Background and Opportunities • Understanding of genome structure provides unprecedented opportunities to define genetic contributions to health and disease, particularly in relation to environmental effects • Progress in application of genomic knowledge to health somewhat hampered by differences between disciplines: • Genetics/genomics • Population-based epidemiology

  12. copy number variants

  13. copy number variants gene deserts

  14. copy number variants gene deserts Bayes Factors HapMap

  15. CEL files copy number variants gene deserts inversion dbGaP calling algorithms Bayes Factors HapMap

  16. anonymized CEL files Q-Q plots clustering algorithms copy number variants HuGENet P3G gene deserts inversion IMPUTATION minor allele frequency population stratification Hardy-Weinberg deviation epistasis whole genome amplification dbGaP calling algorithms ancestral markers linkage disequilibrium Bayes Factors gene-environment interaction HapMap admixture

  17. Larson, G. The Complete Far Side. 2003.

  18. Structure of Session • Bridging epidemiology and genomics (W. Post and D. Nickerson) • Design of initial and replication studies (D. Hunter) • Genotyping platforms and quality control (E. Pugh) • Selection of markers to carry forward (N. Cox) • Managing and analyzing data (L. Scott) • Promoting collaborations (R. Hoover) • Data deposition and access (J. Ostell) • Community concerns (D. Levy) • Data sharing and collaborations (A. Singleton) • Synthesizing findings (M. Gwinn) • Best practices, additional research (Panel)

  19. A Word from Our Sponsor… http://genesandenvironment.nih.gov/

  20. Genes, Environment and Health Initiative (GEI) • NIH-wide initiative of the Secretary, HHS • Aims to accelerate understanding of genetic and environmental contributions to health and disease • Two components: • Genetic analyses of case-control studies of common disease ($26M per year for four years) • Development of innovative technologies to measure environmental exposures, diet, and physical activity ($14M per year for four years)

  21. NHGRI Office of Population Genomics http://www.genome.gov/19518660

  22. NHGRI Office of Population Genomics • Established to facilitate application of genomic knowledge to health, by promoting multi-disciplinary research and applying genomic technologies to population studies • Key goal: Support cross-disciplinary training for geneticists and epidemiologists • Multi-IC Symposia on Application of Genomic Technologies to Population Studies • GWA Studies for the Rest of Us • Designing Geneticists (ASHG, October 2007) http://www.genome.gov/19518660

  23. Many Thanks to SER… Especially Mike Bracken and Peggy Christensen!

  24. Housekeeping Items • Videotaping for webarchive at http://genesandenvironment.nih.gov/, please use microphones during discussion sessions • Two 20-minute breaks and 45-minute lunch • Unable to give you lunch, local lunch list provided • Homework: Closing discussion on best practices and research/tools needed will be of great value to NHGRI and GEI, perhaps SER • Speakers selected for their laid-back genes, ask if you need to know something to go further • There are no stupid questions!

  25. Larson, G. The Complete Far Side. 2003.

  26. Watch for PowerPoints and Video http://genesandenvironment.nih.gov/

  27. Larson, G. The Complete Far Side. 2003.

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