Peter Kerr

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Using informatics to maximise the impact of
cancer research

• Peter Kerr
• NCRI Informatics Unit

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The NCRI Partnership
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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.

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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

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Management Structure
NCRI Board
HLSC
Chair of Informatics Task Force
Task Force
Unit
Data Sharing Committee
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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)
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NCRI Informatics Strategic Partnerships
NCTR
NCRI Informatics Unit
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omics High-throughput techniques

• 30,000 genes

100,000 200,000 proteins
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omics High-throughput techniques

• 30,000 genes

100,000 200,000 proteins
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Tumour response to chemotherapy
Van de Vijver et al, 2002
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Data issues

• Large amount of data
• Lack of data standards
• Lack of interoperability between databases

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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
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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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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
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• 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.

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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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Areas of Focus

• Conceptual Modelling
• Imaging and Pathology
• Clinical Trials and Functional Genomics
• Human Genetic Variation

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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

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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
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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

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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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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.

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• 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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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

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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).

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• 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

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• 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.

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NCTR Overview
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NCRI NCTR Information System Outline Process
Architecture
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