UW-FHCRC Variation Discovery Workshop Schedule

September 8th—September 10th

Monday, September 8th Day One

9:00 am: Introductions and Overview of PGA Program

Candidate Gene Studies (Nickerson)

10:00 am: On-line Resources for SNP Discovery (Rieder)

1.     NCBI LocusLink

a.     Gene Data Outline

b.     Genome Browser Links

1.     NCBI Genome Browser

2.     UCSC Golden Path

2.     dbSNP

a.     Data Setup

b.     Extracting Data

c.     Searching

d.     Data Reliability

3.     GeneSNPs/SNPper

a.     Data Views

b.     Data Extracting

4.     SeattleSNPs

a.     Candidate Genes

b.     Descriptive Text Files

c.     Searching

10:45 am: Break

5.     Participant Candidate Gene of Interest

a.     dbSNP/Locuslink data

b.     GeneSNPs/SNPper data

c.     SeattleSNPs data

 

11:30: Overview of PCR Methods Background and Laboratory Methods (Rieder)

12:00 noon

1:00 pm: Introduction to Software Tools for Sequence Analysis (Rieder)

1.     Phred/Phrap

a.     Basecalling Quality

b.     Sequence Assembly

2.     Consed

a.     Assembly Viewing

b.     Navigation

3.     Polymorphism analysis of sequence data

a.     Using Polyphred

b.     Viewing "Deep" Data with Consed

c.     Viewing PolyPhred information in Consed

Example 1: SNP discovery using Consed

2:15 pm: Break

2:30 pm: SNP verification and tagging

3:00 pm: Applying Variation Data Case Study #1 (Gail Jarvik)

3:45 pm: Applying Variation Data Case Study #1 (Alex Reiner)

4:15 pm: End of Day

 

Tuesday, September 9th

Day Two

 9:00 am: Question/Answer Day One

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

1.     Population Statistics

2.     Examples

 

10:30 am: Break

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

1.     Coalescent Phylogenies

2.     Linkage Disequilibrium

3.     Gene Conversion

 

11:15 am: Applying Data from the PGA Resource (Carlson)

1.     SNP Site Selection

 

12:00 noon: Lunch

 

1:00 pm: Applying Data from the PGA Resource—Haplotypes (Crawford)

1.     Background

2.     Haplotype Estimation Methods

3.     Software tools for Haplotype tagging

2:30 pm: Break

2:45 pm: Applying Data from the PGA Resource (Carlson, Continued)

2.     Population Genetics Software Programs - MEGA

3.     VISTA

 

4:00 pm: End of Day

 

Wednesday, September 10th

Day Three

 9:00 am: Detecting Selection in PGA genes (Akey)

9:45 am: Human Haplotype Map (HAPMAP) & Genotyping Technologies (Nickerson)

10:30 am: Power and Association Studies (Carlson)

11:00 am: Wrap Up Session/Participants Specific Candidate Gene Analysis/Questions