European Genome-phenome Archive database of human data consented for use in biomedical research at the European Bioinformatics Institute

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1 European Genome-phenome Archive database of human data consented for use in biomedical research at the European Bioinformatics Institute Justin Paschall Team Leader Genetic Variation / EGA

2 ! European Genome-phenome Archive! European Variation Archive (EVA)! Clinical Genetics variation databases, data sharing and data discovery 2

3 Most Important Slide https://www.ebi.ac.uk/ega/ 3

4 4

5 Mission of the EGA! Enable collaboration and data sharing of individual patient-level genomic and phenotype data through a controlled-access system. Datasets in scope for EGA are those which are consented for research sharing but cannot be made fully publically available 5

6 What is controlled-access? User discovers a dataset and requests access through an application sent to Data Access Committee (DAC) which governs the study. Request is reviewed by DAC and approved Data is provided by the EGA to user through a secure encrypted channel 6

7 European Genome-phenome Archive (EGA)! Distributed Access Control model! Multiple, study specific Data Access Committees (DACs) Data release policy data access application and data access agreement Each DAC supports tailored data access application process all data users should be named in the application.! EGA supports only data access decisions that are based on the original informed consent! The EGA does not make access decisions, it implements access decisions made by the DACs that manage the data within EGA! Authorized users have personal accounts in our system Access to the data requires account password Data decryption requires a separate key that must be requested and is sent off line

8 Why was the EGA created?! The supporting personally identifiable data may be limited for many reasons National laws Consent agreements Ethical considerations! Data size The 2007 Wellcome Trust Case Control Consortium raw data files are nearly 2 terabytes The 2013 UK10K raw data files will be approximately 200 terabytes Funders, journals, and researchers are reluctant to support broad or mandated data availability without appropriate technical solutions

9 EGA Data scope! Primary archive for any data consented for sharing in the context of research but not for fully public distribution! Raw data from DNA sequencing and array-based genotyping applications, e.g. gene expression experiments, transcriptomics, epigenomics, sequencing or proteomics assays.! Processed datatypes such as genotypes, structural variations or whole genome sequence with any values associated with these calls.! Phenotypic data collected from the subjects and consented for research purpose.! All data must be de-identified and in accordance with the informed consent.! Used for ICGC, IHEC, IHMC, UK10K, DDD and other projects

10 Overview of EGA content! More than 450 studies available for user requests, each ranging from hundreds of thousands of subjects, 4126 users, 400 requests a month.! BAM files, FASTQ, increasing numbers of VCF. 30 TB/month submission! Methods: High throughput array-based genotyping, next gen exome and whole genome, RNA-seq, methylation.! Research domains: Population genetics quantitative traits (WTCCC/ Uk10K), cancer genetics (ICGC/CRUK), rare disease / developmental (Decipher DDD), molecular phenotype (eqtl)! Study meta-data exchange with NCBI, soon more than 1000 studies combined discoverable 10

11 11 UK10K study x coverage whole genome control samples. Exome sequencing of 6000 samples with extreme phenotypes. Rapid data release.

12 12 Finding Datasets in EGA - browse by Data Provider, Study, or Dataset search by accession

13 13 Example of Making a data request - start with UK10K data provider table

14 14

15 15

16 16

17 17

18 18

19 19

20 Data access page (after logging in)

21 For detailed step-by-step instructions for requesting or submitting data see the EGA website. https://www.ebi.ac.uk/ega/about/access

22 22 WTCCC genome wide case-control consortium.

23 23 Rare undiagnosed syndrome exome sequencing

24 24 Cancer Chronic Lymphocytic Leukemia

25 EGA Data Growth EGA data growth / / / / / / / / / / / / / / / / / / / / / / / / / / /01! EGA hosts more than 450 studies and discoverability to the 732 that are in both EGA and dbgap! EGA supports more than 400 user requests per month

26 Future of EGA and ELIXIR! The EGA is a core data resource of the ELIXIR infrastructure and we are piloting developments in collaboration with ELIXIR partners in Finland and Spain Distributed trust authentication system CSC IT Center for Science Institute for Molecular Medicine Finland (FIMM) Establishment of a peer EGA node Centre for Regulatory Genomics Barcelona! Cloud computing! Both FIMM and the CRG are EMBL partner institutes

27 Acknowledgements People! EGA Ilkka Lappalainen, Vasudev Kumanduri, Jeff Almeida-King, Saif Ur- Rehman, Jagasree Kanda! The EBI Variation Team Dylan Splading, Shyamasree Saham Lisa Skipper! The Ensembl Team Funding European Commission Framework Programme 7

28 Submission guide https://www.ebi.ac.uk/ega/submission 28

29 Additional EBI Resources for Variation! Ensembl variation data resources Integrated variation annotation source Multi-species Ensembl Variant Effect Predictor (VEP)! Locus Reference Genomic (LRG) Standard Sequences Reference sequences for reporting and describing genetic variation Clinical diagnostic laboratories and locus specific databases! DGVa (Database of Genomics Variants archive) Structural and copy number variation All species, fully open data Peer database of NCBI s dbvar! European Variation Archive

30 Summary! EGA is a technical solution for secure data storage, management and dissemination. EGA serves large and small data submitters world wide! EGA has a distributed access model and implements decisions made by outside data access committees! Large reference datasets are required to support future biomedical research and personalized medicine EBI provides a number of these reference databases Through ELIXIR some future activities with be integrated and organised across Europe providing worldwide resources Access to the data Data annotation Data integration

31 Four areas of focus Patients - Respect the terms of informed consent, reduce the exposure of identifiable data, provide the tracking and accountability of data use. Make best of use of data to enable medicine Submitting Investigators - Respect the goals and publication timelines, as well as increase the visibility and impact of work of submitting investigators Biomedical Researcher Users Enable science through data sharing: methods development, increases sample size, expand net for rare variants, meta-analysis of raw data. Funders/Consortia - Enable technically feasible, scable, user friendly, and cost efficient solutions to long term archiving and sharing to extract maximum value from these dataset which have been produced through significant investment 31

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