SeattleSNPs Variation Workshop
September 12-13, 2005
This workshop is an introduction to the discovery and use of single nucleotide polymorphism (SNPs) as markers for genetic studies. The course includes sections on the use of human genome sequence databases, annotation of baseline (reference) sequence data, PCR primer selection and methods for SNP discovery, sequencing methods, and the practical application of many software tools needed for SNP discovery. In addition, a series of short lectures will cover approaches to candidate gene studies, an introduction to population genetics principles, the analysis and use of haplotypes, and the selection and use of polymorphic markers for genotype-phenotype analysis. The variation workshop focuses on the latest approaches for identifying SNPs and evaluating associations and linkage disequilibrium with other genetic markers.
September 12: Day 1
Introduction 9:00-9:15 Introduction to SeattleSNPs PGA   (ppt) Debbie Nickerson
Session 1 9:15-10:15 Finding SNPs (part 1)  (ppt)    Mark Rieder
    SNP Discovery methods
    SNP Databases
Break 10:15-10:45
Session 2 10:45-12:00 Finding SNPs (part 2)  (ppt) Mark Rieder
    Database extraction
    Summary characteristics
    SNP analysis
Lunch 12:00-1:15  
Session 3 1:15-2:30 Interactive Tutorial, Day 1: Database Interface (PDF)
    Using the HapMap and Perlegen datasets
    Entrez SNP
Break 2:30-3:00  
Session 4 3:00-4:15 SNP Selection  (ppt)  Dana Crawford
    Linkage Disequilibrium
    Haplotype inference
    Haplotype tagging
    SNP/Haplotype selection methods
September 13: Day 2
Session 1 9:00-10:15 Interactive Tutorial, Day 2: Web Tools (PDF)
    PGA website
    Site selection
    Linkage disequilibrium
    Haplotype analysis
Break 10:15-10:45
Session 2 10:45-12:00 SNP Genotyping  (ppt)  Debbie Nickerson
    Technology platforms
    Data quality control
Lunch 12:00-1:15
Session 3 1:15-2:30 Association Analysis  (ppt)  Chris Carlson
    Study design
    Haplotype analysis vs. SNP analysis
    Analysis methods
    Replication and function
Break 2:30-2:45
Session 4 2:45-4:15 Case Studies