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Peter Kerr

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A Virtual Institute' co-funded by Government & Charities. Focus of activity ... of null or negative findings is pernicious because it skews the results ... – PowerPoint PPT presentation

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Title: Peter Kerr


1
Using informatics to maximise the impact of
cancer research
  • Peter Kerr
  • NCRI Informatics Unit

2
The NCRI Partnership
3
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

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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.

6
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

7
Management Structure
NCRI Board
HLSC
Chair of Informatics Task Force
Task Force
Unit
Data Sharing Committee
8
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)
9
NCRI Informatics Strategic Partnerships
NCTR
NCRI Informatics Unit
10
omics High-throughput techniques
  • 30,000 genes

100,000 200,000 proteins
11
omics High-throughput techniques
  • 30,000 genes

100,000 200,000 proteins
12
Tumour response to chemotherapy
Van de Vijver et al, 2002
13
Data issues
  • Large amount of data
  • Lack of data standards
  • Lack of interoperability between databases

14
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
15
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

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18
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
19
  • SCIENCE TECHNOLOGYClinical trials The
    sounds of silenceSep 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 newsan inconclusive result,
    indicating that the treatment is useless, or a
    negative one, indicating that it is harmfulcan
    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.

20
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

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22
Areas of Focus
  • Conceptual Modelling
  • Imaging and Pathology
  • Clinical Trials and Functional Genomics
  • Human Genetic Variation

23
Platform Reference ModelApproach
  • 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

24
Ethical approval via COREC
Sample Info
Tissue acquisition
MAGE-ML
MGED ontology
Cancer patient
MAGE-OM
Experimenter
MyGrid Services Ontology
ArrayExpress
Data release /access agreement
Microarray Data retrieval
ArrayExpress web services
Scientist
BioMoby
25
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

26
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

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28
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 well-designed 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.

29
  • 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.

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31
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

32
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).

33
  • 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

34
  • 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.

35
NCTR Overview
36
NCRI NCTR Information System Outline Process
Architecture
37
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