ELIXIR
ELIXIR and the Grand Challenges
Janet Thornton
European Life Sciences Infrastructure for Biological Information
www...
A European Infrastructure for
Biological Information
ELIXIR

Genome

Fruitfly

Protein

Cell

Mouse

Embryo

Human
Develop...
The Grand Challenges
• Health
• Changing demographics
• Healthy ageing – extending healthspan
• Infectious diseases

• Agr...
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
ELIXIR
ELIXIR and Health Challenges
Janet Thornton
European Life Sciences Infrastructure for Biological Information
www.el...
Current Human Variation Projects
•
•
•
•
•
•

Many disease cohorts
100,ooo whole genomes in UK
Finnish Project - to sequen...
Variants associated with coronary heart disease
Molecular Basis of Disease
Consequences of mutations

p53 tumour suppressor
core domain - cancers of many types

Cu-Zn Sup...
Heart disease: finding people at risk
• By
, almost
0.5% of our population
is at high risk for
developing heart
disease.
•...
MRSA
• We can use DNA
sequencing to clearly
identify infectious bacteria
• Same technology can
sequence the hospital
envir...
Tracking food-borne pathogens
• 2011 outbreak of E-coli O104:H4
infection
•

responsible for more than 4000 cases
and 50 d...
Designing Novel Alzheimer’s Drugs

Discovery
Target
Discovery &
Validation

Drug
Discovery

Development
Drug
Validation

C...
ELIXIR
ELIXIR and Agricultural Challenges
Janet Thornton
European Life Sciences Infrastructure for Biological Information
...
Impact of genomics on Agriculture & Environment
1

Provision
of reference
genomes

2

Understanding the
genetics
responsib...
Developing Drought resistant varieties
• Drought resistance is a complex
trait, controlled by several genes.
• Identify ge...
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 character...
Breeding robust staple crops
Sustainable bioenergy: genomics and biofuels
development
• Genomics provides a better
understanding of how to harness
vari...
ELIXIR
ELIXIR and Data Challenges
Janet Thornton
European Life Sciences Infrastructure for Biological Information
www.elix...
Future Scale of Genomic Data
1 Human Genome is 109 bases
Human genome for all UK citizens - 65m x 109 = 6x1016
SNPs for al...
Sequencing every child born in the EU?

5 million
births per
year

3 petabytes
of raw data
every day

9
petabases
of DNA
e...
Data islands
?
Data Challenges
Format, Ontologies, Security, Links to clinical records, Data Flow

Infrastructure will be needed to deliv...
BioMedBridges
Ten new biomedical sciences research
infrastructures: stronger through common links
Computational ‘data and...
BioMedBridges
will deliver:
Data bridges


Creating links between available data that were not linked before
will hugely...
ELIXIR
ELIXIR and Innovation
Janet Thornton
European Life Sciences Infrastructure for Biological Information
www.elixir-eu...
ELIXIR & Innovation

DNA as Storage Medium
Interpreting Genomes
Designing new Enzymes
Into the Clinic & Environment
New Dr...
ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 1...
ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 1...
ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 1...
ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 1...
ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 1...
ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 1...
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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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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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ELIXIR and the Grand Challenges presentation given by Dame Prof Janet Thornton, EMBL-EBI Director at ELIXIR launch event 18th December 2013

  1. 1. ELIXIR ELIXIR and the Grand Challenges Janet Thornton European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
  2. 2. A European Infrastructure for Biological Information ELIXIR Genome Fruitfly Protein Cell Mouse Embryo Human Development, Ageing, Disease
  3. 3. 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
  4. 4. We have been living through a revolution.
  5. 5. One genome 2003 to 2013
  6. 6. All living things are made from (DNA, RNA, Protein…)
  7. 7. There has been a huge impact on biological research
  8. 8. We are starting to have an impact on Medicine…
  9. 9. And agriculture, and the environment
  10. 10. ELIXIR ELIXIR and Health Challenges Janet Thornton European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
  11. 11. 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…….
  12. 12. Variants associated with coronary heart disease
  13. 13. 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
  14. 14. 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.
  15. 15. 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
  16. 16. 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
  17. 17. Designing Novel Alzheimer’s Drugs Discovery Target Discovery & Validation Drug Discovery Development Drug Validation Clinical Testing ELIXIR will be involved at every stage – taking care of the data
  18. 18. ELIXIR ELIXIR and Agricultural Challenges Janet Thornton European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
  19. 19. Impact of genomics on Agriculture & Environment 1 Provision of reference genomes 2 Understanding the genetics responsible for agronomic traits Accelerated crop improvement: - quality - yield - disease resistance - changing conditions 3 Future fuels 4 Ecosystem genomics New strategies for pest and disease control Maximising the efficiency of biomass processing Biodiversity management and conservation
  20. 20. 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.
  21. 21. Tomato variation SUN, OVATE, FAS and LC genes make major contributions to differences in fruit shape.
  22. 22. 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.
  23. 23. Breeding robust staple crops
  24. 24. 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.
  25. 25. ELIXIR ELIXIR and Data Challenges Janet Thornton European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
  26. 26. 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
  27. 27. Sequencing every child born in the EU? 5 million births per year 3 petabytes of raw data every day 9 petabases of DNA every week Storing only variants: much more feasible
  28. 28. Data islands ?
  29. 29. 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
  30. 30. 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
  31. 31. 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
  32. 32. ELIXIR ELIXIR and Innovation Janet Thornton European Life Sciences Infrastructure for Biological Information www.elixir-europe.org
  33. 33. ELIXIR & Innovation DNA as Storage Medium Interpreting Genomes Designing new Enzymes Into the Clinic & Environment New Drugs

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