GWAS in a model organism: Arabidopsis thaliana
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GWAS in a model organism:
Arabidopsis thaliana
June 9, 2014
Ashley HintzField Application Scientist
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Use the Questions pane in your GoToWebinar window
Questions during the presentation
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Introduction
Combining topics of previous webcasts:- “Maximizing Public Data Sources for Sequencing and GWAS Studies”- “Back to Basics: Using GWAS to Drive Discovery for Complex Diseases”- “Mixed Models: How to Effectively Account for Inbreeding and Population Structure in
GWAS”
Additional Dimension: Non-human data from A. thaliana
Combining these topics in a single webcast!
+ + =
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Agenda
Obtaining Public Data
Conclusion and Questions
2
3
4
SVS Demonstration
A. Thaliana Data Overview1
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Core Features
Packages Core Features
Powerful Data Management Rich Visualizations Robust Statistics Flexible Easy-to-use
Applications
Genotype Analysis DNA sequence analysis CNV Analysis RNA-seq differential
expression Family Based Association
SNP & Variation Suite (SVS)
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Agenda
Obtaining Public Data
Conclusion and Questions
2
3
4
SVS Demonstration
A. thaliana Data Overview1
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Dataset Overview
Downloaded from Gregor Mendel Institute for Molecular Plant Biology through AtPolyDB
Custom Affymetrix 250K SNP chip
- Genotyped 1307 samples covering 214,051 markers
107 different phenotypes were recorded from Atwell et al. 2010
- Flowering, ionomics, defense and development
Trait associated with virulence to Pseudomonas
www.pseudomonas-syringae.org
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Agenda
Obtaining Public Data
Conclusion and Questions
2
3
4
SVS Demonstration
A. thaliana Data Overview1
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Raw Data
Genotype Data- Downloaded as .CSV file containing
haploid genotypes
- Imported text file to SVS, used Python script to convert to homozygous diploid genotypes for analysis
Sample Data- Text file detailing collection site of all
1307 samples, including GPS coordinates
- Additional text file with phenotypes for 199 samples, as used in Atwell et al. 2010 GWAS paper
- Both were imported to SVS for further analysis
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TAIR_9 Assembly Annotations
Downloaded from Arabidopsis.org
Reference sequence in FASTA format
Gene annotations in GFF3 format
Both converted to SVS native TSF format using tools in SVS
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Agenda
Obtaining Public Data
Conclusion and Questions
2
3
4
SVS Demonstration
A. thaliana Data Overview1
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Demonstration Agenda
EMMAX4
5 Visualizations
Quality Assurance Filters1
Genotype Association Testing3
Principle Components Analysis2
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[Demonstration]
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Agenda
Obtaining Public Data
Conclusion and Questions
2
3
4
SVS Demonstration
A. thaliana Data Overview1
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Conclusion
(Atwell et al. 2010)
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Conclusion
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Questions or more info:
Email [email protected]
Request an evaluation of the software at www.goldenhelix.com