Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .
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Transcript of Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .
![Page 1: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/1.jpg)
Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive
Gary Saunders, PhD
www.ebi.ac.uk/eva
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Agenda
• Overview of European Variation Archive (EVA)
• EVA model of data sharing
• Summary of how we share genetic variation data
• Merging open-access variation datasets
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European Variation Archive – EVA (Eva)
• Curated genetic variation data sharing & analysis platform
• All types of variation:
• SNVs, MNVs, small indels and structural variation
• Germ line, somatic, within / cross population, potentially between speciesSingle portal for open access variation data
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EVA Data Sharing Model
Submitter Archived at EBI
Sample(s) Methodology Genome
EVA
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EVA Data Sharing Model
Submitter Archived at EBI
Sample(s) Methodology Genome
EVA Publication
Collaborators
Wider Study Data
Stable POA Credit for reuse
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EVA: Study Browser
• Core EVA functionality: portal to open-access genetic variation project data (VCF files):
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EVA: Study Browser – project pages
• Core EVA functionality: portal to open-access genetic variation project data (VCF files):
![Page 8: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/8.jpg)
EVA: Study Browser – assessing data quality• Core EVA functionality: portal to open-access
genetic variation project data (VCF files):
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Submission to EVA
• Minimal or data-rich submissions are accepted
• Collaborative process
• Submitter recognition
• Hold date
• Links to runs / experiments / analyses
• Accession number in 48 hours
• EVA has a dynamic study loading pipeline
• Online documentation
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Rate of Submission to EVA
Non-human
Total
March 2014 October 2015
1 billion
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Merging Open-Access Datasets
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share data
Merging Open-Access Datasets
![Page 13: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/13.jpg)
Data submitters
share data
Merging Open-Access Datasets
![Page 14: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/14.jpg)
Data submitters
share data
Merging Open-Access Datasets
![Page 15: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/15.jpg)
Merging Open-Access Datasets
![Page 16: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/16.jpg)
Merging Open-Access Datasets
![Page 17: Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD .](https://reader035.fdocuments.us/reader035/viewer/2022062222/5697bfd81a28abf838caef6b/html5/thumbnails/17.jpg)
Conclusion
European Variation Archivewww.ebi.ac.uk/eva
• Open-access genetic variation archive
• Curated resource
• All types of variants
• All species
• Simplified submission system
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FundingEVAJustin Paschall
Ignacio Medina Castello
Gary Saunders
Cristina Yenyxe Gonzalez
Jag Kandasamy
Ilkka Lappalainen
EGAJeff Almeida-King
Vasudev Kumanduri
Saif Ur-Rehman
Tom Smith
AcknowledgmentsEnsembl VariationFiona Cunningham
Sarah Hunt
William McLaren
Anja Thormann
Laurent Gil
ENARasko Leinonen
Rajesh Radhakrishnan
Daniel Vaughan @ebivariation
www.ebi.ac.uk/eva
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Case-study: deCODE
• Variation data from 2000 Icelanders
• VCF files
• Novel samples and metadata, custom reference genome
• Hold until publication
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Case-study: deCODE
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Case-study: deCODE
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Variant Call Format (VCF): The Community Standard
• Most VCF validation tools do not truly conform to specification:
• Of all ~250 Human VCFs loaded to EVA < 10% were truly valid in first pass
• (EVA has publicized comprehensive C++ VCF validator that raises errors and warnings)
Most VCFs publically available are not truly valid
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Sharing Genetic Variation Data
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• Data accuracy
• Metadata
• Links to associated data
• Credit to data generator(s) for reuse
PROBLEMS
Sharing Genetic Variation Data