NIEHS SNPs Workshop

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

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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)
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• 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

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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

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Pathways
Transcription coupled repair
Mismatch repair
Double strand break repair
Cell cycle
Apoptosis
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Workshop Faculty
Dana Crawford, Ph.D. Mark Rieder, Ph.D Debbie
Nickerson, Ph.D.
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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
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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
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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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