Transcript NCRI Cancer Informatics Initiative - National e

Using informatics to maximise the impact
of cancer research
Peter Kerr
NCRI Informatics Unit
The NCRI Partnership
What is the role of the NCRI?
• Strategic oversight of cancer research in the UK
• Identify gaps and opportunities
• Plan and co-ordinate approaches between funding
bodies
• Monitor progress
• A ‘Virtual Institute’ co-funded by Government &
Charities
• Focus of activity
• Co-ordination and strategic planning
• National Infrastructure issues
The NCRI Cancer Informatics Initiative
• NCRI Board identified cancer informatics as an area
of focus
In this context informatics is defined as the research,
development, or application of computational tools
and approaches for expanding the use of biological,
medical, or health data, including those to acquire,
store, organise, archive, analyse, or visualise such
data.
History
• National Advisory Panel for Bioinformatics met and
developed ‘NCRI Strategic Framework for the
Development of Cancer Research Informatics’
• Strategic Framework approved by NCRI Board
• Funding from CRUK, MRC, DH, ICR, AstraZeneca
• NCRI Informatics Unit established
• Statement of Intent published in Nature and the BMJ
Management Structure
NCRI Board
HLSC
Chair of Informatics
Task Force
Data Sharing
Committee
Task Force
Unit
NCRI Cancer Informatics High-Level
Implementation Steering Committee
Prof Alex Markham (Chair, Chief Executive, Cancer Research UK)
Prof Sally Davies (Director of Research, Department of Health)
Prof Mike Richards (National Cancer Director)
Prof John Williams (Director Health Informatics, Royal Coll Phys)
Prof Colin Blakemore (Chief Executive, MRC)
Prof Mark Walport (Director, Wellcome Trust)
Dr Philip Campbell (Editor-in-Chief, Nature)
Prof Tony Hey (Director, e-Science Core Programme)
Mrs Joanne Rule (Chief Executive, Cancer BACUP)
Professor Alan Horwich (Caldicott Guardian)
Dr Ken Buetow (NCI)
Industry Representative (TBA)
NCRI Informatics & Strategic Partnerships
NCTR
NCRI
Informatics
Unit
‘omics’ – High-throughput techniques
30,000 genes
100,000 – 200,000
proteins
‘omics’ – High-throughput techniques
30,000 genes
100,000 – 200,000
proteins
Tumour response to chemotherapy
Van de Vijver et al,
2002
Data issues
• Large amount of data
• Lack of data standards
• Lack of interoperability between databases
NCRI Strategic Framework for the
Development of Cancer Research Informatics
2 key points:
Common data standards should be
adopted
Data sharing should be
the norm
Progress
• Development of Framework and initial
implementation
• Mapping projects, standards and resources on to a
matrix
• Development of a data sharing policy with the
funders
• Communicating with the community through website,
presentations
Draft NCRI Data Sharing Policy
The NCRI member organisations agree the following:
- Publicly funded research data should be openly available to the maximum
extent possible unless appropriate consent or ethical approval have not been
gained, the confidentiality of study participants can not be safeguarded, or there
are IP issues that are of concern to a potential or existing commercial partner
- In the long-term, all cancer-related research applications should include a data
sharing strategy and NCRI Partners will implement this in a step-wise fashion
over coming academic sessions
- Data should be shared in a timely and responsible fashion
- NCRI Partner Organisations recognise that there may be a cost to allow data
management that enables sharing
- NCRI Partner Organisations will provide applicants with advice on how to
develop a data sharing strategy and recommend that applicants use data use
agreements to govern the use of their data
- NCRI Partner Organisations will assess the validity of data sharing strategies
and monitor their progress as part of their normal review mechanisms
SCIENCE & TECHNOLOGY
Clinical trials
The sounds of silence
Sep 9th 2004
From The Economist print edition
Negative clinical-trial results are underreported. But this may
soon change
SOMETIMES, no news is news. In clinical trials, where new medical treatments are tried out on
human subjects, no news—an inconclusive result, indicating that the treatment is useless, or
a negative one, indicating that it is harmful—can be as scientifically important as a positive
result. Unfortunately, such a result is much less likely to be reported.
That is particularly true for trials sponsored by the pharmaceutical industry which, according to
the American Medical Association (AMA), accounted for over 70% of the funding for such
trials in America in 2002, the most recent year for which figures are available. The lack of
reporting of null or negative findings is pernicious because it skews the results of so-called
“meta-analyses”, which compile data from previous studies of a treatment. If only positive
results are reported, then a meta-analysis risks being too laudatory.
The medical profession has been aware of this problem for a long time. However, pharmaceutical
companies have a vested interest in keeping negative results quiet, so change has been slow
in coming. But the proper balance between commercial confidentiality and public disclosure in
the case of drugs, where ignorance can cost lives through misprescription, is different from
that for, say, computer chips. The widespread government funding of basic drug research also
gives the public a moral claim on the results. And a confluence of forces in the past few
weeks may well succeed in pushing drug companies towards greater openness.
Informatics Website
• www.cancerinformatics.org.uk
• Information resource for the Funders, scientific and
clinical communities and the Unit
• Main point of contact with relevant communities
• The matrix is a unique information resource
• Constantly being updated
Areas of Focus
• Conceptual Modelling
• Imaging and Pathology
• Clinical Trials and Functional Genomics
• Human Genetic Variation
Platform Reference Model
Approach
The first steps in achieving this aim:
• understand what the key components of such a
platform are for different user groups within the
cancer research domain
• to understand what goals this platform is required
to serve for the community and to determine the
feasibility and resources needed
• to understand what resources are available that
can contribute to the construction of the platform
• consider interoperability requirements and how
that might be acheived
Ethical approval via
COREC
Sample Info
Tissue
acquisition
MAGE-ML
MGED
ontology
Cancer
patient
MAGE-OM
Experimenter
MyGrid
Services
Ontology
Microarray
Data retrieval
Scientist
ArrayExpress
Data release
/access
agreement
ArrayExpress
web services
BioMoby
Functional Genomics and Clinical Trials
• Functional genomics community relatively
mature in terms of data sharing
• Clinical trials increasingly incorporating
high-throughput data
• Examining links between genomics,
proteomics and clinical trials disciplines
electronic Remote Data Capture (e-RDC)
Project
• Phase I pilot completed December 2003
- proved e-RDC useful for the collection and storage
of real patient information in a clinical trial
• Phase II will be a multi-centre, multi-trial study to
demonstrate scalability and explore the full
functionality of a clinical data management system
with e-RDC
National Cancer Research Network
• Established to provide the National Health Service
(NHS) with an infrastructure to support prospective
clinical trials of cancer treatments and other welldesigned studies and to integrate and support
research undertaken by cancer charities.
• Its aim is to improve the speed, quality and
integration of research, ultimately resulting in
improved patient care.
• The NCRN is increasing involvement and recruitment
into clinical trials via the creation of 34 cancer
research networks across England, closely aligned to
cancer service networks.
• NCRN funding is allocated to networks to appoint
research staff, such as research nurses, data
managers and medical staff sessions and to access
pharmacy, pathology, radiology and other areas of
support, such as information systems and training, all
of which are integral to high quality research.
National TRAnslational Cancer Research
Network
• A national network of 14 cancer research centres,
embedded in the NHS, that integrates scientific and
clinical expertise, and shares knowledge and
resources for the benefit of cancer patients.
• Initiatives in:
Biotherapeutics
Ethics
Genetics and Genomics Data
NCTR
Working with Industry
Quality Assurance
TuBafrost
National Cancer Tissue Resource
Biology and Treatment Development
• Unified national approach to the large-scale collection of high
quality biological samples linked to clinical outcome data was
needed.
• NTRAC led work on behalf of the NCRI funders to develop
proposals for a National Cancer Tissue Resource (NCTR) –
blueprint produced in 2002
• It is recommended that the NCTR comprises a managed
network of tissue acquisition and processing centres, embedded
within the NHS, underpinned by a state-of-the-art bioinformatics
hub.
• Significant joint funding for the NCTR was announced in 2003
by the Department of Health (DH), the Medical Research
Council (MRC) and Cancer Research UK (CRUK).
NCRI asked NTRAC to take forward 3 key strands of
work to underpin the establishment of the NCTR:
- NCTR is implemented according to highest ethical
standards;
- develop high-level operational framework;
- design and development of the information system
underpinning the NCTR, including NCTR Centre
specification
• The NCTR will facilitate research that advances
cancer therapeutics and diagnostics from the
laboratory to the clinic and will ultimately provide
benefit for UK citizens. This initiative is an important
development for cancer research and depends upon
the willingness of surgical patients to engage with
researchers to combat cancer by donating surplus
surgical samples to the national resource.
NCTR Overview
NCRI NCTR Information System Outline
Process Architecture