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NIEHS SNPs Workshop

Introduction

Debbie Nickerson

Department of Genome Sciences

University of Washington


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


  • The EGP is a multi-component project comprised Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

  • of research in four areas:

  • human DNA polymorphism discovery

  • functional analysis of DNA polymorphism

  • population-based epidemiology studies

  • technology development


  • NIEHS SNPs - Debbie Nickerson, Mark Rieder Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

  • (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)


  • Goals for NIEHS SNPs: Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

  • 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


Chromosome 1 Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

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 Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

Mismatch repair

Pathways

Double strand break repair

Cell cycle

Apoptosis


Workshop Faculty Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

Dana Crawford, Ph.D.

Mark Rieder, Ph.D

Debbie Nickerson, Ph.D.


NIEHS SNPs Workshop Agenda Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

Day 1:

SNP Resources I and II

Mark Rieder and Debbie Nickerson

Interactive Tutorial: Using NIEHS Database Resources

All

SNP Selection

Dana Crawford


NIEHS SNPs Workshop Agenda Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

Day 2:

Interactive Tutorial: Web Tools for SNP Selection

All

SNP Genotyping

Debbie Nickerson

Association Analysis

Dana Crawford

Medical Resequencing

Mark Rieder


Many Thanks! Institute of Environmental Health Sciences (NIEHS), convened a historic conference titled “The Environmental Genome Project” October 17-18 in Bethesda, Maryland

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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