SNP Workshop: Bioinformatics & Genotyping
Presenter: Debbie Nickerson, Ph.D.
Hosts: David Schwartz, M.D., M.P.H. and Samuel Wilson, M.D.
NIEHS Research Triangle Park, North Carolina
January 30-31, 2006
This workshop will provide an overview of the latest approaches for identifying and genotyping single nucleotide polymorphisms (SNPs) and evaluating genetic associations across the human genome. Topics include the extraction of SNP data from public resources, approaches for SNP discovery by re-sequencing, software tools for haplotype inference and optimal SNP selection for genotyping, platform approaches for SNP genotyping, and the analyses of these datasets for genotype-phenotype studies. The workshop will also provide opportunities for hands-on tutorials on a variety of the software tools used for variation analysis.
Registration for the workshop is now closed. There is no charge for the workshop itself; any travel and lodging expenses are the responsibility of the individuals attending the workshop.
Agenda and Presentations
Introduction to Genome Variation(1MB) , (Debbie Nickerson, Ph.D.
Finding SNPs(9MB) (Mark Rieder, Ph.D.)
Brief Review of SNP Discovery Methods
Candidate Gene (NIEHS-oriented) Whole Genome
Finding SNPs(8MB) (Mark Rieder, Ph.D.)
SNP Summary Characteristics
SNP Selection(1MB) (Dana Crawford, Ph.D.)
SNP/Haplotype Selection Methods
Interactive Tutorial I: Database Interfaces (All)(1MB)
dbSNP Using the HapMap, Mark Rieder, Ph.D. - Lead
PolyPhen PolyDoms, Bob Livingston, Ph.D. - Lead
VISTA and ECR
Interactive Tutorial II: Web Tools(386KB) (All with Dana Crawford, Ph.D. - Lead)
SNP Genotyping(6MB) (Debbie Nickerson, Ph.D.)
Whole Genome Data
Haplotype Analysis vs. SNP Analysis
Replication and Function
Medical Resequencing(2MB) (Debbie Nickerson, Ph.D.)
Advanced User Roundtable: High-Throughput Resequencing(3MB)
PolyPhred - Bob Livingston, Ph.D.