1. Sharing Genetic Variation Data via EMBL-EBI: The European Variation Archive Gary Saunders, PhD www.ebi.ac.uk/eva

2. 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

3. 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 species Single portal for open access variation data

4. EVA Data Sharing Model Submitter Archived at EBI Sample(s)MethodologyGenome EVA

5. EVA Data Sharing Model Submitter Archived at EBI Sample(s)MethodologyGenome EVA Publication Collaborators Wider StudyData Stable POACredit for reuse

6. EVA: Study Browser Core EVA functionality: portal to open-access genetic variation project data (VCF files):

7. EVA: Study Browser – project pages Core EVA functionality: portal to open-access genetic variation project data (VCF files):

8. EVA: Study Browser – assessing data quality Core EVA functionality: portal to open-access genetic variation project data (VCF files):

9. 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 eva-helpdesk@ebi.ac.uk

10. Rate of Submission to EVA March 2014October 2015 1 billion

11. Merging Open-Access Datasets

12. share data Merging Open-Access Datasets

13. Data submitters share data Merging Open-Access Datasets

14. Data submitters share data Merging Open-Access Datasets

17. Conclusion European Variation Archive www.ebi.ac.uk/eva Open-access genetic variation archive Curated resource All types of variants All species Simplified submission system

18. Funding EVA Justin Paschall Ignacio Medina Castello Gary Saunders Cristina Yenyxe Gonzalez Jag Kandasamy Ilkka Lappalainen EGA Jeff Almeida-King Vasudev Kumanduri Saif Ur-Rehman Tom Smith Acknowledgments Ensembl Variation Fiona Cunningham Sarah Hunt William McLaren Anja Thormann Laurent Gil ENA Rasko Leinonen Rajesh Radhakrishnan Daniel Vaughan @ebivariation www.ebi.ac.uk/eva

19. Case-study: deCODE Variation data from 2000 Icelanders VCF files Novel samples and metadata, custom reference genome Hold until publication

20. Case-study: deCODE

22. 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

23. Sharing Genetic Variation Data

24. Data accuracy Metadata Links to associated data Credit to data generator(s) for reuse PROBLEMS Sharing Genetic Variation Data