UW-FHCRC Variation Discovery Workshop Schedule

Monday, July 23^rd — Day One

9:00  Overview of Candidate Gene Studies  (Debbie Nickerson)

10:00 am  Generating Baseline (Reference) Sequence for SNP Discovery (Mark Rieder)

1. Human Genome Sequence Databases
1. NCBI LocusLink
2. NCBI Genome Browser
3. UCSC Golden Path
4. Celera Human Genome Data
2. Reference Sequence Annotation
1. Repetitive Sequence - RepeatMasker
2. Exon Mapping — cross_match
3. Visualization — drawmap

11:00 am   Overview of PCR Methods — Background and Laboratory Methods (Nickerson)

12:00 noon Lunch

1:00 pm PCR Primer Selection (Rieder)

1. PCR_Overlap
1. Primer parameters
2. Sequence context problems
2. Fine tuning of primer sets
1. Verification/Mapping — cross_match
2. Primer selection for large candidate genes

2:00 pm Overview of Sequencing Methods (Nickerson)

2:30 pm Introduction to Software Tools for Sequence Analysis (Rieder)

1. Phred/Phrap
1. Basecalling Quality
2. Sequence Assembly
2. Consed
1. Assembly Viewing
2. Navigation
3. Polymorphism analysis of sequence data
1. Using Polyphred
2. Viewing "Deep" Data with Consed
3. Viewing PolyPhred information in Consed
4. SNP identification and verification

5:00 pm End of Day

Tuesday, July 24^th — Day Two

9:00 am Introduction to Software Tools for Sequence Analysis (Rieder)

1. Full Gene Assembly
2. Data Extraction
3. PGA Style Data Presentation

12:00 noon Lunch

1:00 pm Overview of Evolutionary Genetic Analysis (Kruglyak)

2:30 pm Site Selection and Association Studies (Carlson)

4:00 pm Comparative Genomics Analysis VISTA (Rieder)

4:30 pm End of Day

Wednesday, July 25^th —Day Three

9:00 am Overview of PGA - Candidate Gene Analysis

10:00 am Genotyping Technologies (Nickerson)

10:30 am Wrap Up Session — Participants’ Specific Candidate Gene Analysis/Questions