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NIEHS SNPs Workshop Introduction Debbie Nickerson Department of Genome Sciences

NIEHS SNPs Workshop Introduction Debbie Nickerson Department of Genome Sciences University of Washington.

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NIEHS SNPs Workshop Introduction Debbie Nickerson Department of Genome Sciences

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  1. NIEHS SNPs Workshop Introduction Debbie Nickerson Department of Genome Sciences University of Washington

  2. In 1997, Dr. Kenneth Olden, then Director of the National Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland Bold Concept: EGP - Focus on Association Analysis and Environment Precursor of Many Projects: NHGRI - Variation Discovery and HapMap Perlegen 100s of publications using the resources

  3. The EGP is a multi-component project comprised • of research in four areas: • human DNA polymorphism discovery • functional analysis of DNA polymorphism • population-based epidemiology studies • technology development

  4. NIEHS SNPs - Debbie Nickerson, Mark Rieder • (University of Washington) • GeneSNPs - Bob Weiss • Andrew von Niederhausern • (University of Utah) • TraFaC + PolyDom- Bruce Aronow • Anil Jegga • (Children's Hospital Medical Center, • University of Cincinnati)

  5. Goals for NIEHS SNPs: • To identify common sequence variation in genes and pathways that underlie environmental responses • To provide a variation resource for investigators examining the relationships between environmental exposures, inter-individual sequence variation in human genes and disease risk • http://egp.gs.washington.edu

  6. Chromosome 1 3 X > 2% of Genes Mark Rieder Overview: • Variation discovery complete on 626 genes, more than 15 MB of reference sequence • More than 90,000 SNPs identified and genotyped in 90-95 samples; 8.1 million genotypes available • Only 50% of the discovered SNPs previously described • New views being generated to simplify and enhance use by the community

  7. Transcription coupled repair Mismatch repair Pathways Double strand break repair Cell cycle Apoptosis

  8. Workshop Faculty Dana Crawford, Ph.D. Mark Rieder, Ph.D Debbie Nickerson, Ph.D.

  9. NIEHS SNPs Workshop Agenda Day 1: SNP Resources I and II Mark Rieder and Debbie Nickerson Interactive Tutorial: Using NIEHS Database Resources All SNP Selection Dana Crawford

  10. NIEHS SNPs Workshop Agenda Day 2: Interactive Tutorial: Web Tools for SNP Selection All SNP Genotyping Debbie Nickerson Association Analysis Dana Crawford Medical Resequencing Mark Rieder

  11. Many Thanks! Ken Ramos - Director, UofL CGeMM Ted Kalbfleish - Director of Bioinformatics Operations, UofL CGeMM Eric Torskey - UW Liz Maull - NIEHS NIEHS-ES-15478

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