Annual Scientific Report 2015

Justin Paschall
Variation Archive
MA 2008, Washington University St. Louis.
Team Leader at EMBL-EBI from 2012 to 2015.
access datasets, for example a simple yes/no question
as to whether a certain allele exists at a certain position
within a Beacon. We helped develop a tiered-access
beacon that grants an authorised, registered user
access to additional data, such as allele frequencies or
extra datasets. We also co-developed a third level for
controlled access, which serves users who have been
granted full access to specific datasets.
European Variation Archive
In 2016 the number of species represented in the EVA
increased to 22, representing substantial growth in
variation data for animals and plants. Work supported
by the BBSRC and the UK’s Confederation of British
Industry enabled us to offer datasets for plants and
crops, including barley, maize, rice, sorghum and tomato.
Thanks to our participation in the NextGen project
to preserve farm-animal biodiversity, the archive also
offers variation data on animals including cow, goat
and sheep. Other submitted datasets include chicken,
chimpanzee, dog, mosquito, mouse and vervet monkey.
We made available the highly accessed human datasets
from Phase 3 of the 1000 Genomes Project and from the
Exome Aggregation Consortium (ExAC) v0.3.
We improved the Variant Browser in a number of ways,
for example making datasets from 13 different species
more accessible and integrating the variant annotations
generated by the Ensembl’s Variant Effect Predictor
(VEP) tool. To help users detect infrequently occurring
variants with potentially high impact, we updated the
Variant Browser to filter by consequence type, proteinsubstitution
score and minor allele frequency, and to
display population statistics such as allele frequencies.
To guarantee the correctness of submitted data and
improve data quality, we implemented a Variant Call
Format (VCF) validator. Users will be able to download
the results of website queries in VCF format in 2016.
We improved the representation of clinical information
with a new display for data from ClinVar. To support
drug discovery, we also helped standardise ClinVar data,
providing ontology-based representation of disease to
the new Target Validation Platform by Open Targets
(formerly CTTV). In addition, as part of the GA4GH, we
developed global standards and delivered a new API for
archived variation data.
Helen Parkinson
Head of Molecular Archival Resources
PhD Genetics, 1997. Research Associate in
Genetics, University of Leicester 1997-2000.
At EMBL-EBI since 2000.
Future plans
We will complete our work to facilitate access to data in
the EGA by authorised users, enabling them to analyse
these datasets more easily by integrating them with
genome viewers such as Ensembl and open-source
biomedical research platforms such as Galaxy. We will
also extend the downloader to allow access to indexed,
encrypted files. As part of the Accelerating Medicines
Partnership, we will provide federated access to the Type
2 Diabetes Portal. We also plan to develop a new front
end for EGA, improve the submissions workflow, and
optimise file quality control through better feedback
processes with submitters and users.
Funding from the EU-funded CORBEL and ELIXIR-
EXCELERATE grants will enable our team to carry
out important work on establishing standards and
best practice for the secure access to sensitive data.
To allow federated access to the EGA, we will develop
and implement standards for authentication and
authorisation.
Integrating the EGA with EMBL-EBI services including
Ensembl, BioSamples and the ENA will be an important
part of our work in 2016. We will also integrate the
IOBIO visualisation tool to provide more user-friendly
display of file statistics.
The EVA will continue brokering submissions to dbSNP,
saving users an extra step. Including dbSNP data on
multiple species will enable us to connect users with
a catalogue of variation data that submitted through
external services, and all the reference SNP identifiers
(rs) generated by dbSNP.
The EVA will move into a rolling release cycle in 2016,
making datasets available as soon as their processing
is finished. We will improve the performance of the
processing pipeline and the website, creating a better
experience for submitters and end users alike.
Selected publication
Lappalainen I, et al. (2015) The European
Genome-phenome Archive of human data consented for
biomedical research. Nature Genetics 47:692-695
2015 EMBL-EBI Annual Scientific Report 94