Annual Scientific Report 2015

Vertebrate Genomics
The Vertebrate Genomics team works together with the Vertebrate Annotation,
Genome Analysis and Genomics Technology Infrastructure teams to create and
deliver resources of the Ensembl project. It is responsible for data management
for large-scale projects, including BLUEPRINT. It maintains the International
Genome Sample Resource, which incorporates 1000 Genomes Project data, and
the curated NHGRI-EBI GWAS Catalog. These resources are publicly available
and widely used by the scientific community, including members of our team
who conduct research into evolution, epigenetics and transcriptional regulation.
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Vertebrate Genomics is responsible for the scientific
leadership of the Ensembl project, the development
of the Ensembl website and Ensembl outreach and
training. We are also actively involved in the Global
Alliance for Genomics and Health (GA4GH).
Variation Annotation activities in the Vertebrate
Genomics team, coordinated by Fiona Cunningham,
include enriching our part of the GWAS Catalog, which
is created jointly with the Samples, Phenotypes and
Ontologies team. This resource grew substantially upon
migration to EMBL-EBI in early 2015.
Resequencing Informatics, coordinated by Laura
Clarke, provides data coordination activities for many
projects and consortia, including the European Bank for
induced pluripotent Stem Cells (EBiSC), BLUEPRINT
and HipSci. This part of our team also leads the
International Genome Sample Resource (IGSR), which
is a continuation of the 1000 Genomes Project.
Our research projects focus the evolution of
transcriptional regulation, understanding tissue
specificity and annotation of the non-coding genome.
Based on comparative regulatory genomics techniques,
our work provides some of the most definitive results
on how transcription factor binding evolves across the
vertebrate lineage. Our studies of tissue-specific gene
regulation, published in 2015, included clarifying
the role of CTCF, cohesin and other genomic
structural proteins.
Major achievements
Ensembl
We released five comprehensive updates to Ensembl in
addition to a special update of our website supporting
GRCh37, the previous version of the human genome
assembly. In 2015 we focused on improving and
extending four key areas of the Ensembl website: new
views and tools, performance and usability of existing
views, support for track hubs and mirror sites. We
also introduced a new visualisation for long-range
2015 EMBL-EBI Annual Scientific Report
connections between genomic regions such as
enhancer–promoter interactions.
We promoted and facilitated the use of Ensembl
by researchers, clinicians and educators through
97 in-person workshops, conference attendance,
high-quality online training, sustained social media
engagemen and usability testing of new interfaces. We
conducted workshops in several developing countries,
including Colombia, Malawi and Tanzania. We also
held workshops at major conferences including ASHG,
ESHG, PAG and PAGAsia.
Data Management and Coordination
In 2015 we updated the data from several major projects
to reflect the new GRCh38 human reference assembly.
This involved realignment of more than 70 Terabases of
DNA sequence from the 1000 Genomes Project for the
IGSR and updating all BLUEPRINT analyses.
We performed a major upgrade of the HipSci website to
improve the discoverability of individual cell lines and
related information.
We helped launch the Functional Annotation of
Animal Genomes (FAANG) project, which is producing
comprehensive maps of functional elements in the
genomes of domesticated animal species. In this project,
we led efforts to define data and metadata standards to
ensure the outputs will be reusable, well into the future.
Genome-Wide Association
Studies Catalog
We helped relocate the GWAS Catalog software
infrastructure from the National Human Genome
Research Institute (NHGRI) in the US to EMBL-EBI.
The new NHGRI-EBI GWAS Catalog website serves
as a single point of access, and includes an improved
search interface using SOLR technology and supporting
ontology expansion queries. Our curation team adds new
studies to the resource, which now offers data from more
than 2000 studies representing nearly 15 000 SNP–trait
associations.