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GVS: Genome Variation Server
Materials prepared by:
Warren C. Lathe, PhD
www.openhelix.com
Updated: Q2 2010
Version 2
Copyright OpenHelix. No use or reproduction without express written consent 2
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
Copyright OpenHelix. No use or reproduction without express written consent 5
GVS Information
Information about GVS and
contact email
http://gvs.gs.washington.edu/GVS/
Copyright OpenHelix. No use or reproduction without express written consent 6
Four Steps to Results
Choose Data Source (population) Set Parameters View Results
Search Method
Copyright OpenHelix. No use or reproduction without express written consent 7
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/
Copyright OpenHelix. No use or reproduction without express written consent 8
Search Strategies
SearchEntire Database
Search Project Genes
Upload Data
Copyright OpenHelix. No use or reproduction without express written consent 9
Search: Chromosome Location
Choose chromosomeand specific location
Copyright OpenHelix. No use or reproduction without express written consent 10
Search: Gene NameGene name (HUGO)
and upstream or downstreamsequence if wanted
Copyright OpenHelix. No use or reproduction without express written consent 11
Search: Gene IDGene ID (NCBI)
and upstream or downstreamsequence if needed
Copyright OpenHelix. No use or reproduction without express written consent 12
Search: Gene ID
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Gene IDs at Entrez Gene site
abo
Copyright OpenHelix. No use or reproduction without express written consent 13
Search: rs IDrs ID (NCBI)
and upstream or downstreamsequence
Copyright OpenHelix. No use or reproduction without express written consent 14
Search: rs ID
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp
rs IDs found atEntrez SNP site
Copyright OpenHelix. No use or reproduction without express written consent 15
Search: Browse Chromosomes
Clicking gene symbol toopen next steps
Browse to location
Copyright OpenHelix. No use or reproduction without express written consent 16
Search: PGA or EGP GenesChoose gene from menu,
next steps are on the same page
Copyright OpenHelix. No use or reproduction without express written consent 17
Search: Upload Own Data
Upload your own data file
Copyright OpenHelix. No use or reproduction without express written consent 18
Search: Upload Own Data
File Format
SeattleSNPs “prettybase” format: http://pga.gs.washington.edu/data_download.html
Upload File
Copyright OpenHelix. No use or reproduction without express written consent 19
Refining Search
Link returns to search page to expand and refine search
Copyright OpenHelix. No use or reproduction without express written consent 20
Changing Map Location
Click icon to openinteractive map of the region
of your search
Browse to new location, click gene symbol to modify search
Copyright OpenHelix. No use or reproduction without express written consent 21
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
Copyright OpenHelix. No use or reproduction without express written consent 23
Choose Population: Links to Information
Link to dbSNP population record
Link to dbSNP submitter record
Copyright OpenHelix. No use or reproduction without express written consent 24
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/
Copyright OpenHelix. No use or reproduction without express written consent 25
Parameters: Help Section
Links tohelp section
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Parameters: Merge Populations
Merge Population Samples
MultiPop
Copyright OpenHelix. No use or reproduction without express written consent 27
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
Copyright OpenHelix. No use or reproduction without express written consent 30
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/
Copyright OpenHelix. No use or reproduction without express written consent 31
Choose Display Results
Four analysischoices to display
Display
Copyright OpenHelix. No use or reproduction without express written consent 32
Display Genotypes
Parameters SNPs
Ind
ivid
ual
s
Data
Color-coded SNP ID,population sample &
alleles
Table
Graphical
Copyright OpenHelix. No use or reproduction without express written consent 33
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
Copyright OpenHelix. No use or reproduction without express written consent 35
Display SNPs Summary
Summary ofSNP data
Link to dbSNP
Link to UCSC
Genome Browser
Add data columns
Interactive Map
Column Descriptions
Copyright OpenHelix. No use or reproduction without express written consent 36
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.”
Copyright OpenHelix. No use or reproduction without express written consent 38
Choosing Two Populations Data Sets
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Merging Populations
Display Tag SNPs
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TagSNPs Results (Multiple Populations)
Open Table
Copyright OpenHelix. No use or reproduction without express written consent 41
Population 1 Tag SNPs
Open Table
Copyright OpenHelix. No use or reproduction without express written consent 42
Population 2 Tag SNPs
Open Table
Copyright OpenHelix. No use or reproduction without express written consent 43
Graphic Display of Population 1 Tag SNPs
Open Graphic
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Merging Option A Error: No Common Individuals
Display Tag SNPs
Copyright OpenHelix. No use or reproduction without express written consent 45
Populations with Common Individuals
Copyright OpenHelix. No use or reproduction without express written consent 46
Merging Option: Common Individuals
Display Tag SNPs
Copyright OpenHelix. No use or reproduction without express written consent 47
Results: Tag SNPs
Open Table
Copyright OpenHelix. No use or reproduction without express written consent 48
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
Copyright OpenHelix. No use or reproduction without express written consent 50
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
Copyright OpenHelix. No use or reproduction without express written consent 53
Analysis Display
Copyright OpenHelix. No use or reproduction without express written consent 54
Genome Variation Server
Copyright OpenHelix. No use or reproduction without express written consent 55
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
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