Genomic Medicine - Science and Technology Committee Contents



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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