Annual Scientific Report 2015

Variation Archive
Genetic variation represents the individual genomes of studied organisms and
human patients as compared with one another and against the reference sequence
for the species. It is a fundamental data type in molecular biology, population
research and clinical investigation, and our team manages resources that make
it available to researchers worldwide: the European Variation Archive (EVA)
and the European Genome-phenome Archive (EGA).
Human genetic data presents particular challenges
in terms of protecting participant privacy when
individually unique genomes are archived for scientific
research, often requiring controlled-access approval
systems to ensure compliance with data access policies.
The EGA supports secure, controlled-access data
management for human genomes and variation data,
providing a standard mechanism for providing access to
data to a wide set of research users in a secure manner.
It is jointly developed by EMBL-EBI and the Centre for
Genomic Regulation (CRG) in Barcelona, Spain.
EMBL-EBI is a member of the Global Alliance for
Genomics and Health (GA4GH), which partnered
with ELIXIR in 2015 to provide genomics services that
balance data protection and efficient data sharing. The
project develops ‘Beacons’, which provide consent-based
access to genomic data in the EGA as well as national
resources in Finland, Sweden and the Netherlands.
Variation data is the primary analysis product of the
sequencing, alignment and variant-calling pipeline to
studies of population genetics, genotype-to-phenotype
association and functional analysis linking the genome
to molecular pathways. The EVA, the global reference
catalogue of genetic variation, provides a basis for
interpreting each new genome and variant observed in
research and clinical studies. It includes the Database
of Genomic Variant (DGVa) project, provides a primary
archive service for genetic variation data and builds
on EMBL-EBI’s sequence-level archives (i.e. ENA and
EGA), supporting value-added analysis and
visualisation resources.
The European Genome-phenome Archive is
now co-developed with the Centre for Genomic
Regulation in Barcelona, Spain.
Together with international partners, the EVA provides
a stable, accessioned database that catalogues and
provides access to genetic variation in all species. This
is a powerful tool for researchers working in clinical,
agricultural, biotechnological and ecological research.
Major achievements
European Genome-phenome Archive
Our team handled a 50% increase in the volume of
data archived in the EGA and a 65% increase in the
number of files submitted; the resource grew to over
three Petabytes of human genomic and variation
data. We deployed a new EGA downloader service,
which distributed over 1.7 Petabytes of data in 2015. In
collaboration with the GA4GH, we implemented a tiered
Beacon for the EGA, enabling both anonymous and
registered access to a limited collection of variation data.
By being a member of the Beacon Network, multiple
institutions can now easily discover relevant datasets
from a single access point.
We re-built the EGA pipeline to improve capacity and
reliability, and achieved a reduction of the quarterly
average processing time from three weeks to one and
a half days. In the context of the NIH-funded Big Data
to Knowledge (BD2K) project, we exposed variation
data and delivered EGA content for the Omics Data
Discovery Index.
Together with our federation partners and co-developers
at the CRG in Barcelona, we substantially increased the
resource’s capacity to distribute data. The CRG now
distributes files via FTP or Aspera, and EMBL-EBI
distributes files via the EGA downloader. In addition,
a new programmatic interface hosted at CRG provides
access to publicly available metadata about studies,
samples and datasets held in the Archive.
Together with our partners in ELIXIR, the GA4GH
and CRG, we developed a three-tiered Beacon that
provides a single point of access to datasets from
multiple institutions. The Beacon Project allows users
to make simple, anonymous queries on controlled-
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2015 EMBL-EBI Annual Scientific Report