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NIEHS SNPs Workshop Introduction Debbie Nickerson Department of Genome Sciences

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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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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
pathways

Transcription coupled repair

Mismatch repair

Pathways

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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