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ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 18th December 2013
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European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
ELIXIR and the Grand Challenges
ELIXIR
Janet Thornton
A European Infrastructure for
Biological Information
ELIXIR
Genome
Embryo Cell
Fruitfly
Protein
Mouse Human
Development,
Ageing, Disease
The Grand Challenges
• Health • Changing demographics
• Healthy ageing – extending healthspan
• Infectious diseases
• Agricultural • Feeding a growing population
• Food security
• Managing in changing climates
• Environment • Maintaining Biodiversity
• Biofuels
We have been living through a revolution.
One genome 2003 to 2013
All living things are made from (DNA, RNA, Protein…)
There has been a huge impact on biological research
We are starting to have an impact on Medicine…
And agriculture, and the environment
European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
ELIXIR and Health Challenges
ELIXIR
Janet Thornton
Current Human Variation Projects
• Many disease cohorts
• 100,ooo whole genomes in UK
• Finnish Project - to sequence 8000 Finns
• Faroe Islands – to sequence all population (50K)
• German and Spanish large scale cohorts
• International Cancer Genome Consortium - 20,000 high coverage genomes in 5 years for research
• Many others…….
Variants associated with coronary heart disease
Molecular Basis of Disease Consequences of mutations
p53 tumour suppressor
core domain - cancers of many types
Cu-Zn Superoxide
Dismutase - Autosomal dominant
Amyotrophic lateral sclerosis
Heart disease: finding people at risk
• By , almost 0.5% of our population is at high risk for developing heart disease.
• If they knew their risk by , they’d have a chance to beat it.
MRSA
• We can use DNA sequencing to clearly identify infectious bacteria
• Same technology can sequence the hospital environment
• Powerful information for containment response
• “Immune systems for hospitals”.
• Reference resources provided by ELIXIR
Tracking food-borne pathogens
• 2011 outbreak of E-coli O104:H4 infection
• responsible for more than 4000 cases and 50 deaths
• Origin initially linked to cucumbers
• Collaborative genome sequencing to identify pathogen and cause of virulence.
• Origin traced to bean sprouts
Discovery Development
Designing Novel Alzheimer’s Drugs
Clinical
Testing
Target
Discovery &
Validation
Drug
Validation
Drug
Discovery
ELIXIR will be involved at every stage – taking care of the data
European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
ELIXIR and Agricultural Challenges
ELIXIR
Janet Thornton
Provision
of reference
genomes
Impact of genomics on Agriculture & Environment
Accelerated crop
improvement:
- quality
- yield
- disease resistance
- changing conditions
Understanding the
genetics
responsible for
agronomic traits
New strategies
for pest and
disease control
Ecosystem
genomics
Biodiversity
management and
conservation
1 2
4
Future fuels
Maximising the
efficiency of
biomass
processing
3
Developing Drought resistant varieties
• Drought resistance is a complex
trait, controlled by several genes.
• Identify genomic regions
associated with drought
tolerance in wheat – useful in
marker-assisted breeding.
• Re-introducing genes from wild
wheat relatives from the Middle
East into modern varieties.
Tomato variation
SUN, OVATE,
FAS and LC genes
make major
contributions to
differences in fruit
shape.
Sequencing the tomato genome
• Identification of the parts of the
genome responsible for desirable
features and characteristics
responsible for evolutionary success.
• This understanding will lower costs and
accelerate efforts to improve global
tomato production.
• Lead to varieties better equipped to
combat pests, droughts and diseases.
Breeding robust staple crops
Sustainable bioenergy: genomics and biofuels development
• Genomics provides a better
understanding of how to harness
various renewable energy sources,
• Sequencing of potential biofuels:
miscanthus, poplar and willow
• Genetic engineering of enzymes
for optimising the development of
sustainable biofuels.
European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
ELIXIR and Data Challenges
ELIXIR
Janet Thornton
Future Scale of Genomic Data
1 Human Genome is 109 bases Human genome for all UK citizens - 65m x 109 = 6x1016
SNPs for all UK citizens - 65m x 106 = 6x1013 1 petabyte = 1015 EBI currently has ~30 petabytes of storage
3 petabytes
of raw data
every day
9
petabases
of DNA
every week
5 million
births per
year
Sequencing every child born in the EU?
Storing only
variants: much
more feasible
Data islands
?
Data Challenges Format, Ontologies, Security, Links to clinical records, Data Flow
Infrastructure will be needed to deliver the benefit to the patients and also to the academic research and commercial communities will include: • Infrastructure re samples – collection of samples; delivery from hospital to sequencing
centre; delivery of data from sequencing centre to NHS database
• Database to store the genomic data and deliver to users
• Tools to annotate the data
• Generic annotation – by comparison to public reference databases
• Disease specific clinically actionable annotation
• Tools to deliver the data to the clinicians and to integrate data with clinical data
• Tools to provide download of specified data to academics and commercial entities
BioMedBridges
Ten new biomedical sciences research
infrastructures: stronger through common links
Computational ‘data and
service’ bridges between the
BMS RIs
Interoperability between data
and services in the biological,
medical, translational and
clinical domains
Link basic biological research
data with clinical research and
associated data
35
BioMedBridges
will deliver:
Data bridges
Creating links between available data that were not linked before will hugely increase the potential for new discoveries
Interoperability bridges
standards, formats, ontologies... and how to make it linkable!
Social bridges
Connecting the biomedical research infrastructures
Image courtesy of MDOT's Photography
Unit.
European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
ELIXIR and Innovation
ELIXIR
Janet Thornton
ELIXIR & Innovation
DNA as Storage Medium
Interpreting Genomes
Designing new Enzymes
Into the Clinic & Environment
New Drugs