NIEHS SNPs Workshop
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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

NIEHS SNPs Workshop

Introduction

Debbie Nickerson

Department of Genome Sciences

University of Washington


Niehs snps workshop introduction debbie nickerson department of genome sciences

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


Niehs snps workshop introduction debbie nickerson department of genome sciences

  • 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


Niehs snps workshop introduction debbie nickerson department of genome sciences

  • 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)


Niehs snps workshop introduction debbie nickerson department of genome sciences

  • 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


Niehs snps workshop introduction debbie nickerson department of genome sciences

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


Niehs snps workshop introduction debbie nickerson department of genome sciences

Workshop Faculty

Dana Crawford, Ph.D.

Mark Rieder, Ph.D

Debbie Nickerson, Ph.D.


Niehs snps workshop introduction debbie nickerson department of genome sciences

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


Niehs snps workshop introduction debbie nickerson department of genome sciences

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


Niehs snps workshop introduction debbie nickerson department of genome sciences

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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