CHAPTER 5: COMPUTATIONAL USE OF MEDICAL
AND GENOMIC DATA: MEDICAL INFORMATICS AND BIOINFORMATICS
Introduction
5.1. Realising the potential of genomic medicine
will require the storage and interpretation of very large amounts
of genetic information within the NHS, in turn requiring skills
and facilities in bioinformatics and the establishment of information
management systems to link genomic databases with medical patient
records (see paragraphs 2.32-2.36).
5.2. The 2003 Genetics White Paper recognised
the challenges to bioinformatics posed by new genome technologies:
"the prospect of cheap whole-genome scanning could bring
entirely new opportunities. In theory, a patient's whole genome
could be scanned once and the results interrogated later. The
need to store and interpret such vast quantities of computerised
data will produce real challenges in bioinformatics".[23]
5.3. Although the Government's undertakings in
the White Paper (that is, to ensure that genetics was included
in developments in NHS informatics and to develop a genetics portal
on the National Electronic Library for Health) have been met,
the scale of the genomic datasets now being generated in clinical
practice, and the resulting informatics requirements in clinical
genetics and across the NHS, were largely unanticipated. Professor Sir John
Bell told us that:
"Even research labs that have a hold of
the new sequencing technologies are finding it almost impossible
to manage the data … There are two problems. One is that
there is a hardware issue about having the kit to store the information
on. There is also a human capacity problem. Despite the fact that
we all sat around 15 years ago and said that the really crucial
thing to train in the UK will be bioinformaticians—people
who can handle data—the truth is we have now hit the wall
in terms of data handling and management" (Q 461).
The emergence and growth of bioinformatics
5.4. Bioinformatics uses computational methods
to analyse biological data. The discipline has arisen because
of the very large scale of the datasets. A single genome is three
billion nucleotides (see Box 1 in Chapter 2) in length; a typical
genetic experiment analyses a million or more nucleotide sequence
variants or quantitative variation in 25,000 genes. Interpretation
requires not only sophisticated software to format and visualise
the data generated in a particular experiment, but expert programmers
and biologists to work together to develop a comparison with other
data sources, to assess the significance, for example, of a new
sequence variant found in a patient or biological sample. In a
clinical setting, the data need to be presented to clinicians
in a format that will be usable in a near-patient context.
5.5. Bioinformatics is a relatively new discipline,
less than 20 years old. Professor Dame Janet Thornton described
the growth of the European Bioinformatics Institute (EBI):
"There are now about 400 people in the EBI.
This has grown from a size of about 70 when it was started ten
years ago, so this is a huge expansion" (Q 713).
She added:
"within Europe we have an ESFRI (European
Strategic Forum for Research Infrastructures) project called ELIXIR,
which is trying to address the funding for bioinformatics within
Europe and this is a major challenge for us still. We only have
half of our money secured" (Q 712).
5.6. Although the EBI is the European hub for
bioinformatics, these comments highlight the difficulty of securing
sustainable funding for this emerging field. There is a sharp
contrast with the equivalent of the EBI in the United States—the
National Centre for Biotechnology Information (NCBI)—which
"is funded by a direct subvention from Congress. This is
therefore funded at the very highest level and they have a mandate
about what they do there which overrides the biases of individual
clinicians or individual researchers or individual hospitals"
(Q 715).
5.7. The importance of sustainable funding for
the EBI was emphasised by Dr Sir Mark Walport, Director
of the Wellcome Trust:
"In the United Kingdom the holder of much
of [the genomic] information is the European Bioinformatics Institute.
Much of the funding of the EBI is in fact charitable and the European
Union does not provide adequate support for the European Bioinformatics
Institute … It is extremely important that there is national
funding for this enormously important database … I think
one of the major things that this Committee could actually be
helpful on is to point out the need for there to be proper and
sustained funding for databases such as the European Bioinformatics
Institute which will otherwise become unsustainable and would
put Europe in a weak competitive position" (Q 149).
5.8. We recognise the rapid growth in bioinformatics
and its key role in supporting national and European genetics
and genomics activities. Its dependence on charitable and cyclical
EU funding jeopardises the data and the skills base which have
accumulated at EBI over the last ten years. On our visit to the
National Institutes of Health in the United States, we heard that
the large majority of funding for the NCBI was intramural, government
funding.
5.9. We recommend that the Government show
leadership on leveraging sustainable funding to the European Bioinformatics
Institute (EBI), through the European Research Infrastructure
(ESFRI) instrument and through the UK Research Councils. This
would reduce the dependence of the EBI on charitable and cyclical
funding and allow further growth of the Institute commensurate
with the recent growth in genomic databases and the value of the
EBI to the UK science base.
Linking informatics with electronic
medical records
5.10. One of the major challenges of utilising
genomic information within the NHS is linking genomic databases
and informatics platforms with electronic medical records. This
will have benefits both for patients directly by improving patient
care and decision making and indirectly by enabling research for
the public good to unravel the role of genetic, environmental
and lifestyle factors in disease.
5.11. Setting up good electronic patient records
is the first challenge. Dr Kári Stefánsson,
President and Chief Executive Officer of deCode Genetics, told
us that "if you want to let genetics have an impact on your
health care system and if you want to contribute … in advancing
personalised medicine and the use of genetics in medicine, you
have to introduce good electronic medical records into all your
hospitals [and] into your primary care" (Q 548).
5.12. In the UK there has been considerable investment
in creating electronic health records for all patients in the
NHS through the National Programme for IT (NPfIT). In some respects,
progress has been extremely good. Professor Sir Alex Markham
noted that "effectively 100 per cent of NHS patients in primary
care have their records held electronically" (Q 465).
5.13. Electronic patient records hold great value
for research purposes, prescribing practice, pharmacovigilance
and public health. Linking genomic data to electronic patient
records offers additional benefits for patient care and for research.
The Wellcome Trust told us that "the NHS provides a unique
research resource—offering potential to link large-scale
genomic data with information on health outcomes and responses
to treatments captured in electronic patient records" (p 68).
The new Research Capability Programme within Connecting for Health,
the NHS computer programmes that store patients' information,
will help to establish systems to ensure that information is stored
in an appropriate format for research purposes (see QQ 153,
154 and 670).
5.14. Linking these databases will also allow
clinicians to access genomic information to aid their decision-making.
The Wellcome Trust told us that "as genomics research advances
and more clinically-relevant findings result, there will be a
need for resources that collate and present information in a way
that can support clinicians in their decision making. One example
of an existing project is the DECIPHER (Database of Chromosomal
Imbalance and Phenotype in Humans using Ensembl Resources) initiative
at the Sanger Institute, which uses genomic array technologies
to identify chromosome abnormalities in children with developmental
defects and presents this alongside clinical information about
chromosomal abnormality" (p 74).
5.15. But joining electronic health record data
to genetic or genomic data presents considerable challenges. These
were highlighted by the EBI. They include the need to have adequate
safeguards in place to ensure personal data security during data-sharing
(see Chapter 6), the need to consider how to manage and handle
complex genomic datasets within NHS IT systems, and also how the
curators of such databases will handle information on the interpretation
of such data for clinical purposes. Finally, genetic data will
need to be linked to personal medical records to aid decision-making
which will require a complex informatics component. Professor Dame
Janet Thornton told us:
"We feel that genomic medicine is very exciting
and does have enormous potential, and it is really critical, I
think, at this time that the UK addresses the question of how
best to translate this knowledge into the health sector. For us
the informatics challenges that this poses are enormous …
Biomedical informatics … has new aspects that we have not
had to consider within bioinformatics, such as the translation
to the patient, the security of the data, all those aspects are
not a part of our current role, and I think that for the research
at this stage and for the future for the medicine it is clear
that we really do need to strategically plan how to handle these
informatics since it will underpin the future of the translation
into the clinics" (Q 695).
5.16. Dr Ewan Birney, Senior Scientist at
the EBI, drew attention to cultural differences between IT in
the health service, which worked on an "IT procurement kind
of model", and biomedical informatics which is "complex
and … will move and evolve over years requiring more 'a research
style of investment'" (Q 702). Professor Dame Janet
Thornton said that "there are two communities. There are
the bioinformaticians and at the EBI, … we have a very strong
cadre of scientists who address this. We then have the medical
health records area and the electronic health records … and
I do believe that there is something of a gap between the two
and there needs to be a bringing together of these two different
aspects" (Q 696).
5.17. Dr Sir Mark Walport told
us of the excellent organisation of the Tayside healthcare database
and the way in which this has contributed to clinical care and
research: "In Tayside they have a very good electronic database
around diabetes care where the purpose of the database is to provide
better patient care, but that information can also be used in
individuals who have given consent alongside genetic information"
(Q 153). "I have visited the set-up in Dundee and it
is a very powerful set-up in terms of informatics, providing better
patient care and in doing so doing very good research" (Q 172).
5.18. Professor Dame Janet Thornton believed
that, although challenging, it was technically feasible to use
genomic data linked to healthcare records and that a single body
should be tasked with computerising the health records and linking
them to genomic data: "In terms of the investment, I think
it ultimately will be very large … I think we need somewhere
in the UK which has a clear mandate to handle the biomedical records
with that as their priority. This should be linked to the research,
both the clinical research and the biological research, perhaps
in a new institute or in a new unit which would address this"
(Q 701).
5.19. Although it may take time for electronic
health records to become fully established in the UK, the progress
already made, together with evidence of the, albeit smaller, model
in Tayside indicate to us the exceptional long-term value of linking
health records to personal, clinically relevant genetic data,
both for the benefit of basic and clinical research, and for the
long-term value to healthcare of UK citizens.
5.20. The linking of UK electronic patient health
records to personal genetic data would have substantial long-term
value for the health of UK citizens. Given the importance of the
NHS as a resource for clinical trials and genetics research, we
believe that the Government should, as a matter of priority, take
steps to bring together NHS expertise in electronic health records
with the UK's international leadership in genome informatics.
5.21. We recommend the establishment of a
new Institute of Biomedical Informatics to address the challenges
of handling the linking of medical and genetic information in
order to maximize the value of these two unique sources of information.
Such an institute would bridge the knowledge, culture and communications
gap that currently exists between the expertise in NHS IT systems
and bioinformaticians working on genome research. The Institute
would guide the NHS in the creation of NHS informatics platforms
that will interface with databases containing personal genetic
data and with publicly available genome databases.
Developing expertise in bioinformatics
5.22. Given the importance of bioinformatics
to realising the full potential of genomic medicine, it is a cause
for concern that there is reported to be a shortage of expertise
in this area. Dr Elles asked the question: "where are
we going to get the expertise in order to be able to access that
data, to integrate it, and to interpret it at the laboratory level.
We need a whole generation of bioinformatics-trained people …
from the world of bioinformatics to come into healthcare and to
help us interpret this genomic data" (Q 264).
5.23. Professor Sir John Bell drew
attention to the need for "a much more concerted and systematic
approach to making sure that bright young people are brought into
this arena and trained up at a variety of different levels"
(Q 461). Professor Dame Janet Thornton also recognised
the lack of expertise and training in biomedical informatics,
commenting that at the EBI "we run extensive training programmes
in the UK for students and post-docs, and some training of clinical
geneticists has been undertaken, but just a very little bit so
far" (Q 699).
5.24. We recommend that the Department of
Health should establish a centre for national training in biomedical
informatics (within the Institute of Biomedical Informatics) with
the aim of providing training that bridges the gap between health
records information technology and genome informatics, and ensuring
the delivery of an expert workforce for the NHS.
5.25. An important aim of this national training
programme should be to develop, implement and train the healthcare
workforce in the use of secure and stable informatics software
and databases that are suitable for the practice of Genomic Medicine.
(Broader issues relating to the workforce requirements for bioinformatics
within the NHS are considered in Chapter 7.)
Immediate informatics needs of
NHS Regional Genetics Centres and laboratories
5.26. In addition to the long-term need to develop
platforms to interface clinical information with genomic databases,
there is an immediate need to improve the IT and bioinformatics
facilities within the Regional Genetics Centres and laboratories
across the UK in order to store and interpret the enormous amount
of data generated from genetic tests, to aid communication between
laboratories and to allow the comparison of non-personal genetic
information from genomic databases to aid patient care.
5.27. The IT infrastructure of Regional Genetics
Centres was greatly improved by funding following the 2003 Genetics
White Paper. Informatics was not, however, a high priority in
the White Paper, and there is now an urgent requirement for more
bioinformatics expertise and tools.
5.28. Dr Elles told us that the need was
immediate:
"Increasingly … we find variants in
the DNA sequence of patients and we are not always sure what that
variant means so it is the task of the laboratory scientist to
try and interpret that by comparing whether for example that variant
has been seen in another laboratory in the UK … [or] …
much further afield … The tools which we have [to do this]
… have been developed for research use … often there
is very little quality assurance in the data … Yet we are
starting to need to use them for healthcare in the patient care
pathway. [The] tools … are often unstable, by which I mean
the research funding ends … and we are left high and dry
in terms of not having a tool that is useful for healthcare"
(Q 264).
5.29. Other witnesses, for example, the Institute
of Medical Genetics (IMG) and UKGTN, pointed out that software
for clinical genetics needs to be developed since there is no
nationally available software for displaying family history. Although
progress has been made in Wales and the National Genetics Reference
Laboratory in Manchester has done some good work, "funding
for the local implementation of LIMS [Laboratory Information Management
Systems] is left up to individual Trusts, so it is patchy, and
risks inefficiency and inequality" (p 248). Also, network
communication speeds needed urgent improvement. Dr Crolla
commented on his work with Connecting for Health:
"The problem was that through the NHS N3,
the band width out to the Internet was 250 kb/sec speed width
for the whole of the NHS, for all 1.2 million users … [I
understand that it is currently] one megabit per second, …
[but] it urgently needs upgrading to much faster, ten or 20, or
as the French are now installing in Paris 100 megabits per second
as a standard broadband band width … This technology infrastructure
improvement should [not] only be in the reference laboratories.
I think it should be in all laboratories which are accessing genomic
information" (Q 210).
5.30. We see clear deficiencies in the informatics
tools and communication bandwidth available to the Regional Genetics
Centres and National Genetics Reference Laboratories and note
that funding for informatics in this area is patchy due to local
implementation.
5.31. We recommend that the Department of
Health should implement a programme of modernisation of computing
and information technology within the Regional Genetics Centres
and laboratories, including an upgrade in computer hardware, software
tools and communication bandwidth, in order to manage current
needs of clinical and genome informatics in the Regional Centres.
23 The 2003 Genetics White Paper, p 28, para 2.22. Back
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