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

Slides:

Advertisements

Similar presentations

Asthma One child in 10 in the EU Childhood asthma costs the EU 3 Billion p.a. Adult and industrial asthma also 3 Billion Abnormal airway mucosa Intermittent.

Advertisements

The Human Genome Project

On bad genes and how to detect them (Game from Univ. Utah)

The DNA Bead String Exercise Anita L DeStefano, PhD Department of Biostatistics BU School of Public Health Co-Director Biostatistics Program Associate.

Outline to SNP bioinformatics lecture

Variation Workshop University of Washington March 20-21, 2006 Sponsored by the NHLBI.

Predicting the Function of Single Nucleotide Polymorphisms Corey Harada Advisor: Eleazar Eskin.

Genome-Wide Association for the Rest of Us: Introduction and Goals National Human Genome Research Institute National Institutes of Health U.S. Department.

Computational Tools for Finding and Interpreting Genetic Variations Gabor T. Marth Department of Biology, Boston College

Introduction to Genomics, Bioinformatics & Proteomics Brian Rybarczyk, PhD PMABS Department of Biology University of North Carolina Chapel Hill.

The Extraction of Single Nucleotide Polymorphisms and the Use of Current Sequencing Tools Stephen Tetreault Department of Mathematics and Computer Science.

Bioinformatics Student host Chris Johnston Speaker Dr Kate McCain.

Picking SNPs Application to Association Studies Dana Crawford, PhD SeattleSNPs PGA University of Washington March 20, 2006.

SNP Resources: Finding SNPs, Databases and Data Extraction Debbie Nickerson NIEHS SNPs Workshop.

BI420 – Course information Web site: Instructor: Gabor Marth Teaching.

SNP Resources: Variation Discovery, HapMap and the EGP Mark J. Rieder Department of Genome Sciences NIEHS SNPs Workshop Jan 10-11,

SNP Resources: Finding SNPs Databases and Data Extraction Mark J. Rieder, PhD Robert J. Livingston, PhD NIEHS Variation Workshop January 30-31, 2005.

BME 130 – Genomes Lecture 23 Genome evolution I: Mutations, repair, and recombination.

Introduction of Cancer Molecular Epidemiology Zuo-Feng Zhang, MD, PhD University of California Los Angeles.

Polymorphisms – SNP, InDel, Transposon BMI/IBGP 730 Victor Jin, Ph.D. (Slides from Dr. Kun Huang) Department of Biomedical Informatics Ohio State University.

Single nucleotide polymorphisms and applications Usman Roshan BNFO 601.

SNP Selection University of Louisville Center for Genetics and Molecular Medicine January 10, 2008 Dana Crawford, PhD Vanderbilt University Center for.

SNP Resources: Finding SNPs Databases and Data Extraction Mark J. Rieder, PhD SeattleSNPs Variation Workshop March 20-21, 2006.

University of Utah Department of Human Genetics Pharmacogenomics Louisa A. Stark, Ph.D. Director.

Introduction to the NIH Grants System

Polymerase Chain Reaction WORKSHOP (3)

Selecting TagSNPs in Candidate Genes for Genetic Association Studies Shehnaz K. Hussain, PhD, ScM Assistant Professor Department of Epidemiology, UCLA.

Haplotype Discovery and Modeling. Identification of genes Identify the Phenotype MapClone.

Special Topics in Genomics Lecture 1: Introduction Instructor: Hongkai Ji Department of Biostatistics

Design Considerations in Large- Scale Genetic Association Studies Michael Boehnke, Andrew Skol, Laura Scott, Cristen Willer, Gonçalo Abecasis, Anne Jackson,

Georgia Wiesner, MD CREC June 20, GATACAATGCATCATATG TATCAGATGCAATATATC ATTGTATCATGTATCATG TATCATGTATCATGTATC ATGTATCATGTCTCCAGA TGCTATGGATCTTATGTA.

RExPrimer Pongsakorn Wangkumhang, M.Sc. Biostatistics and Informatics Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology.

Cincinnati Comparative Mouse Genomics Centers Consortium: Bioinformatics Analysis Tools for Assessment of Human Gene Polymorphisms Anil G Jegga, Sivakumar.

Epigenome 1. 2 Background: GWAS Genome-Wide Association Studies 3.

Introduction to BST775: Statistical Methods for Genetic Analysis I Course master: Degui Zhi, Ph.D. Assistant professor Section on Statistical Genetics.

Detecting enriched regions (Chip- seq, RIP-seq) Statistical evaluation of enriched regions Data displayed in Genome Browser Detection of enriched motifs.

The NIEHS Environmental Genome Project: Enabling Studies of Gene-Environment Interaction Douglas A. Bell, Ph.D. Environmental Genomics Section National.

Sequencing TRAF1 in patients with rheumatoid arthritis Bruce C. Jobse Medical and Population Genetics Broad Institute.

Single Nucleotide Polymorphisms Mrs. Stewart Medical Interventions Central Magnet School.

Computational research for medical discovery at Boston College Biology Gabor T. Marth Boston College Department of Biology

The Center for Medical Genomics facilitates cutting-edge research with state-of-the-art genomic technologies for studying gene expression and genetics,

Regulation of Gene Expression: An Overview  Transcriptional  Tissue-specific transcription factors  Direct binding of hormones, growth factors, etc.

Introduction of Department of Molecular Biology for Public Health in SCDC Ye Lu Shanghai Municipal Center for Disease Control & Prevention Shanghai Institute.

©Edited by Mingrui Zhang, CS Department, Winona State University, 2008 Identifying Lung Cancer Risks.

Biology 101 DNA: elegant simplicity A molecule consisting of two strands that wrap around each other to form a “twisted ladder” shape, with the.

VarDetect: a nucleotide sequence variation exploratory tool VarDetect Chumpol Ngamphiw 1, Supasak Kulawonganunchai 2, Anunchai Assawamakin 3, Ekachai Jenwitheesuk.

DNA TECHNOLOGY AND BIOTECHNOLOGY PAGES Chapter 10.

SeattleSNPs Variation Discovery Resource Materials prepared by: Mary E. Mangan, PhD Updated: Q Version 1.

Personalized Medicine Dr. M. Jawad Hassan. Personalized Medicine Human Genome and SNPs What is personalized medicine? Pharmacogenetics Case study – warfarin.

By: Dr. M. M. O. Okonji FRCPsych. (UK) Consultant Psychiatrist.

Julia N. Chapman, Alia Kamal, Archith Ramkumar, Owen L. Astrachan Duke University, Genome Revolution Focus, Department of Computer Science Sources

Using a Single Nucleotide Polymorphism to Predict Bitter Tasting Ability Lab Overview.

Epidemiology 217 Molecular and Genetic Epidemiology Bioinformatics & Proteomics John Witte.

TOXICOGENOMICS.

The International Consortium. The International HapMap Project.

Association of functional polymorphisms of Bax and Bcl2 genes with schizophrenia Kristina Pirumya, PhD, Laboratory of Human Genomics and Immunomics Institute.

Copyright OpenHelix. No use or reproduction without express written consent1.

Using a Single Nucleotide Polymorphism to Predict Bitter Tasting Ability Lab Overview.

As discoveries of genetic polymorphisms in the human population expand, so does the opportunity and challenge of correlating these with disease-risk. Thus,

Analyzing DNA using Microarray and Next Generation Sequencing (1) Background SNP Array Basic design Applications: CNV, LOH, GWAS Deep sequencing Alignment.

A Librarian’s Guide to NCBI. The Course provided… B asic knowledge and skills for librarians interested in helping patrons use online molecular databases.

Human Genomics Higher Human Biology. Learning Intentions Explain what is meant by human genomics State that bioinformatics can be used to identify DNA.

Using public resources to understand associations Dr Luke Jostins Wellcome Trust Advanced Courses; Genomic Epidemiology in Africa, 21 st – 26 th June 2015.

1 Finding disease genes: A challenge for Medicine, Mathematics and Computer Science Andrew Collins, Professor of Genetic Epidemiology and Bioinformatics.

Gil McVean Department of Statistics

Consideration for Planning a Candidate Gene Association Study With TagSNPs Shehnaz K. Hussain, PhD, ScM Epidemiology 243: Molecular.

Genome organization and Bioinformatics

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

SNPs and CNPs By: David Wendel.

Presentation transcript:

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 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 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 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: 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

Variation discovery complete on 626 genes, more than 15 MB of reference sequence More than 90,000 SNPs identified and genotyped in 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 1 3 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 Selection All SNP Genotyping Debbie Nickerson Association Analysis Dana Crawford Medical Resequencing Mark 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 Many Thanks!