SeattleSNPs Variation Workshop
March 20,and 21, 2006
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.
March 20: Day 1
Introduction 9:00-9:15 Introduction to the Workshop, PGAs and SeattleSNPs  (ppt) Debbie Nickerson
Session 1 9:15-10:15 Finding SNPs, Pt. I  (ppt)  Mark Rieder
    SNP Discovery methods
SNP Databases
Break 10:15-10:45
Session 2 10:45-12:00 Finding SNPs, Pt. II  (ppt) Mark Rieder
    Database extraction
Summary characteristics
SNP analysis
Lunch 12:00-1:15  
Session 3 1:15-2:45 Interactive Tutorial, Day 1: Database Interface (PDF)
Using the HapMap and Perlegen datasets
Entrez SNP
Break 2:45-3:00  
Session 4 3:00-4:30 SNP Selection  (ppt)  Dana Crawford
    Linkage Disequilibrium
Haplotype inference
Haplotype tagging
SNP/Haplotype selection methods
March 21: Day 2
Session 1 9:00-10:30 Interactive Tutorial, Day 2: Web Tools (PDF)
    PGA website
Site selection
Linkage disequilibrium
Haplotype analysis
Break 10:30-10:45
Session 2 10:45-12:15 SNP Genotyping  (ppt)  Debbie Nickerson
    Technology platforms
Data quality control
Lunch 12:15-1:30
Session 3 1:30-3:00 Association Analysis  (ppt)  Chris Carlson
    Study design
Haplotype analysis vs. SNP analysis
Analysis methods
Replication and function
Break 3:00-3:15
Session 4 3:15-4:45 Case Studies
    Polymorphism in the C Reactive Protein and plasma CRP levels (Crawford)  (ppt)