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UW-FHCRC Variation Discovery Workshop Schedule

July 15rd — July 17th, 2002


Click on highlighted links to view slide presentations


Monday, July 15rd — Day One

9:00   Introduction and Overview of PGA Program  (Debbie Nickerson)

10:00 am  Online Resources for SNP Discovery (Mark Rieder)

  1. NCBI LocusLink
    1. Genome Browser Outline
    2. Genome Browser Links
    1. NCBI Genome Browser
    2. UCSC Golden Path
  2. dbSNP
    1. Date Setup
    2. Extracting Data
    3. Searching
    4. Data Reliability
  3. SNPer
    1. Data Views
    2. Data Extracting
  4. Seattle SNPs
    1. Candidate Genes
    2. Descriptive Text Files
    3. Searching

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

12:00 noon Lunch

1:00 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. Using PolyPhred
    1. Viewing "Deep" Data with Consed
    2. Viewing PolyPhred Information in Consed
    3. Example 1: Basics of Consed
    4. Example 2: Joining
    5. Example 3: Full Gene Assembly

Tuesday, July 16rd — Day Two

9:00 am  Question/Answer: Day One

9:30 am  Applied Analysis for Genetic Data (Carlson)

  1. Population Statistics
  2. Examples

10:45 am  Introduction to Statistical Population Genetics (Eberle)

  1. Mutation Process
  2. Coalescent Phylogenies
  3. Linkage Disequilibrium

11:30 am  Applying Data from the PGA Resource (Carlson)

  1. Viewing Data: Visual Genotypes
  2. Haplotype Estimation

12:00 noon  Lunch

1:00 pm  Applying Data from the PGA Resource (continued)

  1. SNP Site Selection
  2. Population Genetics Software Programs

4:00 pm  End of Day

Wednesday, July 17th — Day Three

9:00 am  Candidate Gene Analysis (Nickerson)

9:45 am  Genotyping Technologies (Nickerson)

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

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