GVS: Genome Variation Server
Materials prepared by:
Warren C. Lathe, PhD
www.openhelix.com
Updated: Q2 2010
Version 2
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GVS Agenda
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
Copyright OpenHelix. No use or reproduction without express written consent 3
Genome Variation Server at SeattleSNPs
http://pga.gs.washington.edu/
The Genome VariationServer: a project of
SeattleSNPs
Copyright OpenHelix. No use or reproduction without express written consent 4
Access to Genome Variation Server
http://pga.gs.washington.edu/
access GVS
access GVS
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GVS Information
Information about GVS and
contact email
http://gvs.gs.washington.edu/GVS/
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Four Steps to Results
Choose Data Source (population) Set Parameters View Results
Search Method
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GVS Agenda: Search
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
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Search Strategies
SearchEntire Database
Search Project Genes
Upload Data
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Search: Chromosome Location
Choose chromosomeand specific location
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Search: Gene NameGene name (HUGO)
and upstream or downstreamsequence if wanted
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Search: Gene IDGene ID (NCBI)
and upstream or downstreamsequence if needed
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Search: Gene ID
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Gene IDs at Entrez Gene site
abo
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Search: rs IDrs ID (NCBI)
and upstream or downstreamsequence
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Search: rs ID
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp
rs IDs found atEntrez SNP site
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Search: Browse Chromosomes
Clicking gene symbol toopen next steps
Browse to location
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Search: PGA or EGP GenesChoose gene from menu,
next steps are on the same page
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Search: Upload Own Data
Upload your own data file
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Search: Upload Own Data
File Format
SeattleSNPs “prettybase” format: http://pga.gs.washington.edu/data_download.html
Upload File
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Refining Search
Link returns to search page to expand and refine search
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Changing Map Location
Click icon to openinteractive map of the region
of your search
Browse to new location, click gene symbol to modify search
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GVS Agenda: Populations
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
Copyright OpenHelix. No use or reproduction without express written consent 22
Choose Population Data Source
Select population
Data merging
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Choose Population: Links to Information
Link to dbSNP population record
Link to dbSNP submitter record
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GVS Agenda: Parameters
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
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Parameters: Help Section
Links tohelp section
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Parameters: Merge Populations
Merge Population Samples
MultiPop
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Parameters: Sorting Data
Sort data by position or ID
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Parameters: Table or Text
Display data in a variety of formats
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Parameters: SNP Filtering, Clustering, Colors
Filter
Cluster
Tag SNPs
Plot Color
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GVS Agenda: Analysis Results
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
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Choose Display Results
Four analysischoices to display
Display
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Display Genotypes
Parameters SNPs
Ind
ivid
ual
s
Data
Color-coded SNP ID,population sample &
alleles
Table
Graphical
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Display Tag SNPs
Parameters
Data SNPs clustered by r-squared
LD valuesIn
div
idu
als SNPs
bin
bin
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Display Linkage Disequilibrium
Parameters
Data
R-squared values forall pairs of SNPs LD Plot
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Display SNPs Summary
Summary ofSNP data
Link to dbSNP
Link to UCSC
Genome Browser
Add data columns
Interactive Map
Column Descriptions
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GVS Agenda: Merging Populations
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
Copyright OpenHelix. No use or reproduction without express written consent 37
Merging Populations & Tag SNPs: Example
Click gene name
http://gvs.gs.washington.edu/GVS/
Click Search
“Determine tag SNPs for genotyping variations
with a minor allele frequency of greater than 20% in the
ABO gene for both the PGA European
& PGA African populations.”
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Choosing Two Populations Data Sets
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Merging Populations
Display Tag SNPs
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TagSNPs Results (Multiple Populations)
Open Table
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Population 1 Tag SNPs
Open Table
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Population 2 Tag SNPs
Open Table
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Graphic Display of Population 1 Tag SNPs
Open Graphic
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Merging Option A Error: No Common Individuals
Display Tag SNPs
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Populations with Common Individuals
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Merging Option: Common Individuals
Display Tag SNPs
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Results: Tag SNPs
Open Table
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GVS Agenda: Summary
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
Copyright OpenHelix. No use or reproduction without express written consent 49
Genome Variation Server
http://pga.gs.washington.edu/
The Genome VariationServer is a project of
SeattleSNPs
access GVS
access GVS
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Eight Search Possibilities
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Several Data Sources to Choose
Select population
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Limit and Refine Results
Filter
Cluster
Tag SNPs
Plot Color
Output
Merge
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Analysis Display
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Genome Variation Server
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GVS Agenda: Summary
Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises
Genome Variation Server: http://gvs.gs.washington.edu/GVS/
Copyright OpenHelix. No use or reproduction without express written consent 56