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