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

EnvironmentPrecursor of Many Projects:

NHGRI - Variation Discovery and HapMapPerlegen

100s of publications using the resources

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 - Debbie Nickerson, Mark Rieder (University of Washington)

GeneSNPs - Bob WeissAndrew von Niederhausern

(University of Utah)

TraFaC + PolyDom- Bruce AronowAnil Jegga

(Children's Hospital Medical Center,University of Cincinnati)

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

• 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

Overview:

Chromosome 13 X

> 2% of Genes

Mark Rieder

Pathways

Mismatch repair

Double strand break repair

Apoptosis

Cell cycle

Transcription coupled repair

Workshop Faculty

Dana Crawford, Ph.D.

Mark Rieder, Ph.D

Debbie Nickerson, Ph.D.

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

Day 2:

Interactive Tutorial: Web Tools for SNP SelectionAll

SNP GenotypingDebbie Nickerson

Association AnalysisDana Crawford

Medical ResequencingMark Rieder

NIEHS SNPs Workshop Agenda

Ken Ramos - Director, UofL CGeMM Ted Kalbfleish - Director of

Bioinformatics Operations, UofL CGeMM

Eric Torskey - UW

Liz Maull - NIEHS

NIEHS-ES-15478

Many Thanks!