Cancer Research UK turns to the cloud to support Race For Life site demand

We know a couple of the guys who worked on the revamp of Cancer Research UK's Race for Life site, we watched them passing a toy fish round their scrum meetings and tolerated their thieving of desk-space and chairs from our team - but we didn't know that they had been using cloud-based services to support the massive demand for access to their new site - read more at the Cloudcircle.

Informal response from the National Cancer Intelligence Network - and Department of Health framework for Cancer Intelligence

We had some informal feedback on our response (we know, it was too long for a blog post!) to the National Cancer Intelligence Network's (NCIN) consultation document yesterday - in passing, a colleague from the NCIN, with no hint of irony! indicated that they had taken three key points from it which were:

• Skills and experience in eHealth need nurturing in the UK
• Data quality is the key to driving usage
• To maintain an awareness of the potential for duplication of effort and spend in their proposals

We also promised you a link to the Department of Health's report An Intelligence Framework for Cancer - published 13th December 2011: "High quality care is critical to improving cancer outcomes. While this country has many of the elements required to collect, analyse and publish information; there are also deficiencies in cancer intelligence. This document sets out plans to tackle these deficiencies and sets out aspirations."


The document was produced by the NCIN, following a commitment made by the Department of Health to the Public Accounts Committee in May 2011. 


In case you are not aware: "The NCIN is a UK-wide initiative working to drive improvements in standards of cancer care and clinical outcomes by improving and using the information collected about cancer patients for analysis, publication and research."

Response to the National Cancer Intelligence Network's consultation: Building an e-health research infrastructure for cancer

Today is deadline day for responses to the National Cancer Intelligence Network's (NCIN) consultation: Building an e-health research infrastructure for cancer (see our blog entry for a list of their proposals).

We have submitted a response from the perspective of those who have worked with data supporting basic and translational research - we'll also be posting later a link to the NCIN and Department of health publication from December last year: An Intelligence Framework for Cancer - but for now, here's how we replied to the consultation:

The UK is currently supporting or considering the development of several initiatives seeking to promote the skills and infrastructure necessary to carry out health research based on linked large-scale or population-level datasets generated through routine processes of data collection.

In Wales, the Health Information Research Unit at the University of Swansea maintains the Secure Anonymised Linkage System (SAIL); in Scotland, the Scottish Health Informatics Programme (SHIP) supports the “collation, management, dissemination and research analysis of anonymised Electronic Patient Records”; in the UK, the Research Capability Programme of the National Institute for Health Research have piloted a Health Research Support Service which is due to be formally implemented as a full service:  the Clinical Practice Research Datalink. The Medical Research Council also recently issued a call for e-Health Informatics Research Centres to “maximise the health research potential offered by linking electronic health records with other forms of routinely collected data and research datasets”.

Of the National Cancer Research Institute partners’ 2010 funding, however, over 50% was spent on research which could be described as basic, translational or early stage; 40% on Biology and Aetiology alone; and some proportion of the discovery and development elements of spending under Common Scientific Outcome (CSO) 5 (Treatment), technology development and evaluation under CSO 4 (Early Detection, Diagnosis and Prognosis), and CSO7 (Scientific and Model Systems) can be ascribed to these types of research.

The infrastructure used to support this work is in many cases intra-institutional, in some inter-institutional, rather than national – although with appropriate standardization, integrated datasets from within institutions could be submitted to national-scale repositories with greater ease. Completeness, accuracy and granularity of the data are vital for this research. Often the data which support and contextualize observations in the laboratory during these research projects are drawn from multiple hospital systems and collated with difficulty. This has an impact on timescales and the validation of observations. Some proportion of the NCRI partners’ spend in each of the CSOs is dedicated to Resources and Infrastructure (R&I) which may include informatics, however, if we look at the other project types falling under R&I for e.g. CSO 4 (Early Detection, Diagnosis and Prognosis) we may reasonably conclude that the proportion dedicated to informatics is not the majority – closer analysis of the NCRI CaRD database is required to confirm this.

CSO4.4 Examples of science that would fit: ·         Informatics and informatics networks; for example, patient databanks ·         Specimen resources (serum, tissue, images, etc.) ·         Clinical trials infrastructure ·         Epidemiological resources pertaining to risk assessment, detection, diagnosis, or prognosis ·         Statistical methodology or biostatistical methods ·         Centers, consortia, and/or networks ·         Education and training of investigators at all levels (including clinicians), such as participation in training workshops, advanced research technique courses, and Master's course attendance. This does not include longer term research based training, such as Ph.D. or post-doctoral fellowships

The MRC, in their call for e-Health Informatics Research Centres, adduce the key findings of the ABPI and UK research funders mapping exercise reviewing the UK capability in e-Health records research – a number of these can be applied to the intra-institutional situation:: institutions could be submitted to national-scale repositories with greater easeics is not the

·         There is a shortage of people with the breadth of skills necessary to carry out the complex linkage and analyses required in health informatics research.

·         There is an absence of career structure in enabling roles such as data managers, software engineers, informaticians and data analysts.

·         There are no clear interfaces between researchers and industry, policy makers or the NHS and there is no ready means for sharing best practice.

Certainly, my own experience of supporting even institutes with strong reputations for research is that they lack the skills, focus and confidence in informatics to make much progress in the development of their infrastructure – and have been extremely glad of the opportunity to take advice and receive support from experienced individuals with a research and informatics background.

Perhaps the NCIN could consider devoting some resource to skills development in this area, disseminating the acquired expertise and knowledge of the NCIN of best practices in data management and handling and the use of technology. Might this sit alongside the work currently envisaged by Proposal 6 of the consultation?

_________

During a meeting with Oracle at the end of last year, an ex-colleague who specialises in molecular and gynaecological oncology suggested that their institute would not be seeking data integration services and infrastructure supply from the likes of Oracle with such urgency if they felt they could get ‘stage and grade’ at diagnosis from the Thames Cancer Registry.

The paucity of staging data in the registries is an established weakness as discussed in the NCIN and Department of Health document, An Intelligence Framework for cancer and steps are being taken to address this, however, the perception of the inadequacy of the dataset collected by the Thames Cancer Registry (and by extension, despite shining examples such as the ECRIC, the amalgamated registries’ dataset) extended beyond the known weaknesses unfairly to the dataset as a whole in the case of this Professor. Such perceptions were not uncommon at that centre and need to be overturned.

The vastly extended dataset which will be collected by the registries in future sounds extremely promising in its potential to support not only epidemiological and population-level research, but also basic and small-scale clinical research. It will be vital, however, to create a sustained ‘sales’ initiative to establish a new level of confidence in the data in the areas of the research community who have hitherto not engaged with these datasets due to the concerns described in An Intelligence Framework. Their concern may be that where a smaller dataset was found wanting, will the collection of a larger one not push already stretched resources beyond their elastic limit?

Having had first-hand experience of the way in which MDT data is fed into the Somerset system and the ample opportunities, often taken by overburdened MDT co-ordinators, to introduce error – it is inspiring to see that a truly modern approach to data extraction and aggregation is being implemented as described by Dr. Rashbass at, to give one instance, the NOCRI Information Systems Workshop.  As described by Dr. Rashbass, various technologies including natural language querying will take data from pathology full-text reports, from local imaging systems and myriad other systems to create the amalgamated national dataset – and this data will be quality controlled and assured. More information on how the latter will be achieved would be welcome.

Similar initiatives and technologies are being employed by healthcare delivery and research organisations themselves – for example, the ORIS oncology platform being implemented intra-organisationally by King’s Health Partners and the Acropolis platform being implemented inter-organisationally. It is important to note that these implementations may be beyond the budget of smaller organisations who deliver oncology services and conduct research – and here the value of a new ‘high-resolution’, quality assured, timely dataset such as that envisaged by the registry modernisation team will have the potential to deliver enormous benefit.

But this will depend on the quality of the data and ensuring that this quality is recognised in the research community. “This service will ensure that common standards and working practices are applied to data extraction, linkage and quality assurance to both national feeds and a range of local sources.” This assertion really needs to be backed up with a strong communications and ‘marketing’ effort.

To this end, should the NCIN devote some resource to support activities at the provider end of the process to ensure that where providers are implementing their own data infrastructures, these can interface with and provide bulk data to the unified registries to the appropriate standard; and where they are not yet capable of developing their own infrastructures, that they have support in the provision of accurate and complete data to the registries and potentially support in the process of designing their own data architectures and integration solutions; and then to effectively communicate the work that they are doing to improve registry data effectively to the community – concentrating not on the sophisticated use of technology to capture and amalgamate data, but on the procedural changes being implemented to assure quality?

Many of the proposals made in the consultation document might be realised by the same infrastructural components – and many of these components are similar to those which will hopefully be implemented by the Clinical Practice Research Datalink (CPRD). Where respondents to the consultation indicate that the proposed data linkage and notification services would deliver great benefit to their work, it may be worth establishing what level of awareness they have of the CPRD, the concern being that the overhead involved in creating facilities which might duplicate some aspects of the CPRD could be enormous given the proportion of the budget for the latter initiative devoted to infrastructure. There might be a greater return on investment to be had by focusing on data rather than infrastructure at the national level?

In conclusion, it might be worth considering if Proposal 6 (a research support service advising on the availability of and access to data) could benefit from being expanded to include some work looking at supporting data quality and intra-institutional infrastructural development -  and engaging the basic and translational research communities to overturn perceptions about the ability of the dataset to support their work.

Let us know what you think - are we way off-beam?

Cancer Research UK unites with global research groups (IRCI and EORTC) to fight rare cancers

We missed this press release from Cancer Research UK last week - the only other place we've seen it publicly is on ecancermedicalscience in their Insider News section:


Cancer Research UK will ... join forces with international research groups from the UK, Europe and the US to launch an initiative to boost the development of new treatments for patients with rare cancers. The announcement will be made by Dr Harpal Kumar, chief executive of Cancer Research UK, at the 2011 World Cancer Leaders’ Summit taking place today in Dublin.

The International Rare Cancers Initiative (IRCI) has been established by Cancer Research UK and the National Institute for Health Research Cancer Research Network (NCRN) in the UK, the National Cancer Institute (NCI) in the US, and the European Organisation for Research and Treatment of Cancer (EORTC).

The initiative will design and fund clinical trials of treatments for rare cancers – defined as those which occur in approximately fewer than two cases per 100,000 people. There are limited treatment options for patients suffering with these cancers and there is an urgent need to develop new therapies.

Initially the IRCI will focus on designing clinical trials for five cancer types: salivary gland cancer, small bowel adenocarcinoma, gynaecological sarcoma, ocular melanoma (melanoma of the eye) and penile cancer.

Helene Craddock, 37, a nurse in the intensive care unit at Bristol Children’s Hospital, was diagnosed with cancer of the salivary glands at the age of 19. She said: “Being told you have cancer is a very difficult thing to come to terms with.  You have a lot of questions, which is normal, but having a rare cancer means the answers are not always there. “I am very thankful to say that although I had extensive surgery, and continue to be followed up, I am currently very well.

“There is a huge need to look into these rarer cancers, and I sincerely hope that this new research will lead to improvements in understanding, diagnosing and treating these cancers, and ultimately give us all more hope for our futures.”

The first clinical trial developed as a result of the IRCI, a study for patients with a type of gynaecological cancer called uterine leiomyosarcoma, has recently received approval from both the NCI and Cancer Research UK.  Nine further studies are currently being developed through the initiative. The partner organisations will provide the funding that will enable patients in their countries to take part in the studies.

In addition, it is hoped that studies for other rare cancer types will be developed through the IRCI, including studies in anaplastic thyroid cancer, fibrolamellar hepatoma, thymoma and metastatic/relapsed anal cancer.

Dr Harpal Kumar, chief executive of Cancer Research UK, said: “This initiative is an exciting opportunity for some of the top clinicians in the world to work together to develop and run trials for rare cancers. We hope this will lead to new and more promising treatments for those patients who today have a very limited set of options.

“This is an urgent need. New treatments for rare cancer types are few and far between – these essential clinical trials are the first step in helping these cancer patients. International collaboration is critical to share knowledge and expertise in this area – it will help speed up and improve the design of these trials. We hope this initiative will increase survival from these diseases.”

Professor Matt Seymour, director of the NCRN, said: "Although each rare cancer may affect only a small number of patients, for those people it is critical that we find the best treatments. And combined, rare cancers affect thousands of UK patients every year.

“But research has lagged behind common cancers, partly because rare cancers have not been a priority for drug companies and funders, and partly because it is difficult to organise large-scale trials in diseases only affecting a few patients in any one region.

"Over the past decade, Cancer Research UK and the NCRN have led the world in making cancer research part of routine treatment in every hospital: over 46,000 UK patients took part in NCRN trials last year. We are confident that by bringing together experts from around the worldwe can do ground-breaking research, even in these rare diseases."

Ted Trimble, director of NCI's Center for Global Health, said: “This initiative will allow us to perform trials for cancers so rare that none of us could have managed it on our own.  Working together like this allows us to reduce the cost of trials for each partner organisation, to speed development and conduct of rare cancer clinical trials, and to harness worldwide expertise in these rare conditions.”

Denis Lacombe, EORTC headquarters director, said: “The low numbers of patients with rare tumours brings an urgent need for international cooperation of experts with complementary skills and knowledge to find new ways to treat these diseases.

“This International Rare Cancers Initiative will allow cancer doctors to recruit patients for one large and effective trial, instead of several smaller trials whose results might be inconclusive.

“EORTC embraces this initiative. Rare tumors are a priority at EORTC, which has carried out landmark trials that have changed standard of care for rare cancers such as glioma and sarcoma.

“Patients and public health are at the center of the EORTC mission, and this initiative fits perfectly into the EORTC scientific agenda.”

Notes: 

The following eight rare cancers currently form the core activities of the IRCI.  The names of the lead clinicians for each rare cancer have been listed:

Head and Neck cancer specifically;

Salivary gland cancer 

Leads: Dr Kevin Harrington (UK), Dr Alan Ho (US), Dr Lisa Licitra (EORTC)

Anaplastic thyroid cancer

Leads: Dr Laura Moss (UK), Dr Keith Bible (US), Professor Martin Schlumberger (EORTC)

Small bowel adenocarcinoma

Leads: Dr Richard Wilson (UK), Dr Rob McWilliams (US), Dr Arnaud Roth (EORTC)

Gynaecological sarcoma

Leads: Dr Helen Hatcher (UK) Dr Martee Hensley (US), Professor Jean-Yves Blay (EORTC)

Fibrolamellar hepatocellular carcinoma

Leads: Dr Tim Meyer (UK), Dr Marcio Malogolowkin (US), Dr Michel Ducreux (EORTC)

Penile cancer

Leads: Dr Steve Nicholson (UK), Dr Curtis Pettaway (US), Dr Christine Theodore (EORTC)

Ocular melanoma

Dr Ernie Marshall (UK), Dr Richard Carvajal (US), Professor Poulam Patel (EORTC)

Thymoma

Professor Mike Lind (UK), Professor Frank Detterbeck, Dr Sanjay Popat

Metaplastic/relapsed anal cancer

Dr Rob Glynne-Jones (UK), Dr Al Benson (US), Professor Dirk Arnold

Consultation on building an e-health research infrastructure for cancer

The National Cancer Intelligence Network (NCIN) posted a consultation document on their site last week to coincide with the beginning of the National Cancer Research Institute's annual conference.

It's worth reading this in conjunction with the Department of Health document describing the new Clinical Practice Research Datalink which we blogged about a few days ago as the consultation seeks to co-ordinate its proposals with the infrastructure developments proposed by the CPRD.

In overview (taken from the Executive Summary - these are expanded upon in the main body of the document) the proposals are:

Proposal 1: A safe haven facility to enable research access to potentially identifiable data from the English cancer registration service in a secure, controlled environment. All outputs removed from the safe haven would be checked against anonymity criteria before release.

Proposal 2: A linkage service to allow combination of different datasets for use in research.

Researchers with the appropriate consent could receive data from the cancer registration service to supplement a study dataset. Other researchers could receive access to the de‐identified product of linking one or more existing datasets to cancer registry data.

Proposal 3: A notification service for new cancer diagnoses and other events.

Investigators could register study participants (with their consent) with the cancer registration service and allow them to be regularly informed of new diagnoses and other events.

Proposal 4: A hosting service for study data. This would provide investigators with a secure environment in which to store and analyse their study data together with routinely collected information from the cancer registration service.

Proposal 5: Support for the planning and recruitment of studies.

This would involve mechanisms for estimating trial feasibility and the likely recruitment rates of different centres, and for notifying clinical teams when patients are eligible for a particular study or clinical trial. (Potentially a joint project with the NIHR Cancer Research Network (NCRN) and others).

Proposal 6: A research support service. This would advise users on the availability of data, the requirements for access, and would manage requests and provide access.

Proposal 7: Guidance on guidance on permissions for data access and linkage.  

This would involve providing investigators with guidance on consent wording for using record linkage and notification services. (Potentially joint projects with NRES and NIGB and others).

National Cancer Research Institute's 2011 Conference

In case you are not already following on Twitter (#NCRI2011) or the blog (http://scienceblog.cancerresearchuk.org/) the NCRI conference is in full swing in Liverpool. Unfortunately we're not able to attend this year but we'll be looking out for choice updates to collate and talking to some of our colleagues about the highlights as it progresses.

eCancermedicalscience.com are blogging about it already and quite fulsomely: http://ecancermedicalscience.com/blog.asp?postId=171

Best wishes to all involved.

Application of CancerGrid Technologies to Translational Research

We're nearing the end of our summary of the day's Information Systems workshop courtesy of NOCRI but there's still plenty to cover!

Dr James Brenton, Group Leader at CRUK’sCambridge Research Institute, was one of the day’s pro-caBIG speakers. Wemanaged to jot down some of the nitty-gritty, CancerGrid SQIV integratesclinical and lab data (e.g. TMA slides) using inference rules to create XMLrepresentations of both for the purpose of modeling analytical software andinterfaces. Some of the tech used has been borrowed from Astrogrid who usejava-based tools to manipulate the vast quantities of data necessary fromresearch into the universe. From what we can recall, the CancerGrid andPathgrid softwares will be open and reusable - this is the abstract of Dr.Brenton’s talk:

“CancerGrid is an initiative involvingscientists at the Universities of Oxford and Cambridge, working together to reducethe cost of clinical research, and to increase its value through effective datasharing. It is building upon the success of a four-year project funded by theUK Medical Research Council, to address a wider range of scientific goals, withsupport from Microsoft Research. The CancerGrid team have developed standardsand tools for the automatic production of the systems needed to supportclinical studies and translational research. The vision:

· the researcher createsa model of their study or dataset, based upon standard templates, using asimple study designer tool

· the software artefacts- forms and services - needed to run the study, or interact with the dataset,are then produced automatically from the model

The production process works toimplement exactly the support required through the configuration of familiar,trusted software applications, such as Microsoft Office with SharePoint, or theopen-source eXist XML database - applications that are used throughout the UKNHS, in government, and in industry. Along with a meta-model (or modeltemplate) for clinical studies, based upon the CONSORT statement, and work onthe classification and registration of clinical trials, the project hasproduced an ISO11179-compliant metadata registry, a semantically aware trialsdesign/ management system, and a toolkit for clinical data transformation andintegration. These models and software applications have been tested throughinitial deployment on a small number of clinical studies in Oxford andCambridge. The metadata registry software has been adopted for use within theUS caBIG initiative, and is being evaluated by a number of organisations withinthe UK. Development continues at Oxford, with clinical collaboration inCambridge and London, and technical collaboration with the caBIG team in theUS.”

NIHR / NOCRI Information Systems Workshop - Part 5 - The Oncology Research Information System (ORIS)

We were fortunate enough to speak to Prof. Peter Parker (Cancer Theme Lead, NIHR BRC at Guy’s and St Thomas’ NHS Foundation Trust & King’s College London) prior to the day beginning in earnest and he is as approachable and engaged in person as you could hope - and, having previously blogged about ORIS we were  really looking forward to getting the inside scoop on the system.

IDBS have pulled this system together using Custodix for pseudonymisation, ORION for integration (also see this interesting eHealth Insider article on ORION's acquisition of Microsoft Amalga), HTB ETS(Oralce Healthcare Transaction Base Enterprise Terminology Service) as a terminology service and Inforsense ClinicalSense for the clinical data- the set-up includes a bespoke software toolbox for analysis and the system is currently in UAT at Guy's and St. Thomas's.

To fill you in on what the system does - here is the abstract for Prof. Parker's talk:

"ORIS is an IT platform that enables the routine extraction of consented, structured clinical data (notes, images, etc), its pseudonymisation and export into a research data store, from which patient cohorts can be selected and their information linked to molecular data derived from research. The development of ORIS has been driven by the compelling need to enrich the value of the extensive molecular analysis of patients and in the case of oncology of the somatic changes associated with the development and progression of cancer. It is expected that the benefits derived from a deeper understanding of the relationship between biomolecular events and response to treatment will be improved early detection (selective screening), new interventions, better patient stratification, improvement in patient quality of life and better outcomes."

NIHR / NOCRI Information Systems Workshop - Part 4 - The English National Cancer Registration Service As a Source of Research Data

Dr Jem Rashbass, National Director for Cancer Registry Modernisation based at the Eastern Cancer Registration and Information Centre, spoke so fluently (and persuasively) that we found it hard to put pen to paper except to note that the natural language query tool his team have been using is TinQL (pronounced ‘tinkle’) – which converts natural language queries into SQL – but we’ve been able to find precious little on this tech on the web so perhaps we’ll follow that up with Dr. Rashbass and get back to you.

He also stated that trying to get a variety of institutions to provide data in a standard format on standard media and with exactly the same variables is not a process with which he wished to engage – so all of the processing is done very smartly at the receiving end and ultimately a data feedback process ought to encourage some stepping up to the mark by data suppliers.

The abstract for Dr. Rashbass’s talk was:

“The National Cancer Information Network is leading a change management programme across the English Cancer Registries to implement a single National Cancer Registration Service by the end of 2012. The NCRS is based on the Encore computer system and working practices of the Eastern Cancer Registry and Information Centre (ECRIC) and delivers near-real-time, clinically-rich quality assured information on all 350,000 cancers diagnosed in England. The Service will be run as a managed network across the existing eight local cancer registries. Data collection by the National Cancer Registration Service is covered by permissions from the National Information Governance Board; patient-identifiable information is available from nearly twenty different types of local and national information sources. The Service infrastructure of the National Registry has been developed to support a variety of national initiatives including the new national cancer audits in breast and prostate cancer and the CRUK stratified medicine initiative.”

NIHR / NOCRI Information Systems Workshop - Part 3 - The Cancer Research UK Stratified Medicine Programme in Informatics

It was great to see Monica Jones, recently appointed Informatics Lead at Cancer Research UK (CRUK), who spoke about the potential to scale the CRUK Stratified Medicine Initiative up to national level and on their “connect all” rather than “replace all” strategy which will focus on the use of standards and facilitation of interoperability. Monica flagged up a forthcoming CRUK informatics ‘connectathon’ which sounds really interesting.

The abstract for Monica’s talk is below:

“The CR-UK Stratified Medicine Programme will ultimately deliver a multi-site system for the access and analysis of routinely collected cancer clinical and genetic data. Phase one which has just started, will capture and store the appropriate data from 9,000 cancer patients consented in the next two years. It seeks to utilise existing Experimental Cancer Medicine Centres (ECMCs) data capture capability and XML messaging for rapid molecular diagnostic data transfer between hospitals and labs. It will also will extract and link datasets (to the NHS National Data Standards) in a central repository provided through a partnership with the Eastern Cancer Registry which is fully compliant with NHS Information Governance regulations. In parallel, the Technology Strategy Board (TSB) is funding the development innovative analytical applications that will complement this, thus providing an overall strategic direction.”

NIHR / NOCRI Information Systems Workshop - updates to come

We'll be blogging in greater depth on the NOCRI Information Systems workshop this afternoon - but just to tantalise... it was a really inspirational day which showcased a great deal of talent and achievement in the bioinformatics arena - and arrived at some concrete actions which the NIHR will be taking forward - watch this blog later today...

NIHR NOCRI Information Systems Workshop - Achieving Advances in Translational Informatics

Look out for our updates on Monday evening when we will be blogging on the highlights of the NOCRI Information Systems Workshop - here's some background from the NIHR events pages:

This workshop hosted and organised by the NIHR Biomedical Research Centres at South London and Maudsley NHS Foundation Trust and Guy’s and St Thomas’s NHS Foundation Trust, in collaboration with NOCRI, will focus on:

• Facilitating research applications of electronic medical records.
• Enhancing clinical informatics research capacity through data linkage.
• Dealing with large variable datasets and multiple data sources.

 The aims of the workshop are to:

• Share successful innovations and best practice in informatics research and infrastructure developments for experimental medicine and translational and clinical research;
• Identify opportunities for working together to address common challenges that limit capacity for developing and executing multidisciplinary clinical translational studies across the translational research landscape;
• Identify opportunities for enhancing capacity for experimental medicine and translational clinical research through linkage or integration of complementary approaches to the collection, management, analysis and dissemination of large-scale heterogeneous biomedical data sets.

Of particular interest to us will be the IT demonstration of the Open Clinica Electronic Data Capture and Clinical Data Management System by the NIHR BRC at Oxford Radcliffe Hospitals NHS Foundation Trust - and also the talk on The Oncology Research Information System (ORIS) [which we have previously blogged about] by Professor Peter Parker Cancer Theme Lead, NIHR BRC at Guy’s and St Thomas’ NHS Foundation Trust & King’s College London

So what tools are European Bioinformaticians using? Part 1

We blogged at the end of September about an article in ecancermedicalscience covering a paper which documented usage of caBIG tools and technologies by European researchers - the basic findings of the repot were that the tools are not widely used (these are tools designed to produce "an integrated informatics grid to incorporate open source, open access tools to collect, analyse and share data, enabling everyone to use the same methods and language for these tasks") but that where they are, they are very highly rated.

The feedback we had when we spoke to some friends at caBIG was that this was no big surprise as their efforts had been directed at the US biomedical enterprise and they had not made any serious investment in promoting their offering in Europe...

We thought the headline of the article ("European cancer researchers failing to use research tools") might raise a few eyebrows with other friends of ours at research institutes across the UK who most certainly are using research tools - so we thought we'd set about finding out what tools are available in Europe and who is using what.

First stop, the European Bioinformatics Institute - OK, so they don't focus on cancer, but the tools they offer clearly have an application in various aspects of cancer research - in their own words, the most popular of them "include tools for the analysis and comparison of nucleotide and protein sequences, data from functional genomics experiments, text mining of the scientific literature and tools for determination and visualisation of macromolecular structures. All these tools can be accessed over the web and most provide Web Services interfaces using SOAP orREST APIs."


For more detail, see the EBI tools page - but in summary, they offer tools covering:

• Nucleotide sequence searches x2 (across various database including EMBL-Bank, Coding Sequences, immunoglobulins and High throughput cDNA)
• Protein sequence searches x2 (across database including UniProtKB, sequences derived from macro molecular structures, immunoglobulins and sequences from patents)
• Multiple sequence alignment tools x5!
• Pairwise sequence alignment tools x2
• Functional genomics tools x3
• Potein function analysis tools x4
• Molecular structural analysis tools x2
• Scientific literature text mining tools x2
• And five data retrieving and ID mapping services:
• • dbfetch
  • ENA / SRA
  • ENA / EMBL-SVA
  • UniProt / UniSave
  • SRS
  • PICR

Over the next week we are going to look in more detail at some of the tools being used in the UK from micro-array technologies to clinical data management systems - including those from the EBI listed above - and how these are being linked to derive new insights...  use any yourself which you particularly rate? Then let us know!

CRUK Report – environment for medical research & Simon Denegri's blog

We posted recently about the CRUK report Building the Ideal Environment for Medical Research but without much in the way of comment.

Contrast with Simon Denegri's blog post on the report which makes for interesting reading - the views he expresses chime largely with our own - as we've noted beneath his analysis.

These two paras from the report give you a taste of the content:

"The external policy environment has significant influence on the strength of research. This is particularly relevant in an extremely challenging public funding climate. This report outlines mechanisms for UK governments to demonstrate clear commitments to medical research, and enhance the environment in which it is conducted, enabling [CRUK] to maximise [their ]potential to deliver economic growth as well as ultimately leading to improvements in the health of the nation.

The report draws upon the experience of thirty Cancer Research UK experts, including [their] researchers and in-house professionals with expertise in research funding and strategy, with whom [they] conducted in-depth interviews. [They] considered how the following elements are needed to build a thriving medical research environment: funding; infrastructure; collaboration; investing in people; regulation and governance.”

And this from Simon Denegri summarises our own thoughts!: "I can’t quite get rid of a nagging feeling that it would have been great if it had gone just that little bit further."

UK Cross-organisational personalised medicine platform in development

We blogged a few days ago about ORIS, a cross-organisational research platform linking clinical, pathology, sample and genetic data for research and care provision purposes - being implemented by the Integrated Cancer Centre at King's Health Partners.

Somewhat belatedly, we've also come across another development at King's which involves linking this intra-organisational platform to an external team creating inter-organisational datasets for translational research - is this the future? - we hope so.

Enterprise breadth IT Platform ORIS to support personalised cancer care

Ahead of the NOCRI Information systems workshop on the 17th October, we were researching some of the speakers and their organisations and came across ORIS, a cross-organisational research platform linking clinical, pathology, sample and genetic data for research and care provision purposes - being implemented by the Integrated Cancer Centre at King's Health Partners.

It occurred to us that for centres without the IT spend to support such an implementation, a virtualised offering with the same capabilities, centrally hosted by a major organisation such as Cancer Research UK would enable smaller institutions to link their data repositories across pathology, genetics, clinical systems and would also facilitate central aggregation (by agreement, of course) across institutions to derive novel linked datasets for research.... any thoughts?

Prognostication in cancer

We're blogging from a mobile today so links are at the bottom of this post.

Thanks to our friends at the and the National Cancer Research Institute for directing us to these two articles in the British Medical Journal.

The first is a research paper whose abstract states the objective of the prospective study as being: "To develop a novel prognostic indicator for use in patients with advanced cancer that is significantly better than clinicians’ estimates of survival."

Looking at the prognostic value of a number of clinical and laboratory observations in 1018 patients with advanced or metastatic cancer referred for palliative care, they were able to determine a number of variables predictive of two week and two month survival with equal or greater accuracy than clinicians' estimates.

The responses address data which might further illuminate these findings and patient responses to being given survival estimates.

The second is an editorial (extract of which is free to read if your network does not enable you to get full access) referring to this research whilst lamenting the current state of prognostication as a skill in healthcare.

Having worked at one tertiary referral centre (Bart's in London) where prognosis was discussed with patients often on the basis of a database of the patient population for that centre going back thirty years it's interesting to reflect on how unique that facility was.

National Cancer Intelligence Network

Research paper from the BMJ Editorial from the BMJ

Industry and academic reports - New page

We're getting there - 15 documents so far - suggestions welcome!

These are the better known documents from a trawl covering the spectrum of web-pages, journal articles and major reports – these include several reports from the Academy of Medical Sciences, DoH white papers, reports from or commissioned by the Research councils, strategic plans from funders of research in the UK, the Health Survey for England, reviews on data sharing, reviews of patient and professional perspectives on the use of personal information in medical research and statements regarding the economic importance of biomedical research from both government ministries and independent commentators.

We already have a few more lined up to go on today - let us know your views - see the new page above Useful Industry Reports.

NCRI Informatics publishes catalogue of clinical databases

DoCDat, a UK catalogue of clinical databases, has been given new life by the National Cancer Research Institute Informatics Initiative (NCRI INI).

DoCDat is a seminal catalogue of clinical databases in the UK from which the NCRI INI have selected the seventy databases containing data on cancer cases to publish through their Resource Catalogue.

Created and launched by researchers from the London School of Hygiene and Tropical Medicine in 2001, one of the aims of the initiative was to help realise the potential of clinical datasets to support evaluative research by providing independent evidence as to the uses and limitations of each resource in the directory.

The catalogue provides information about security and confidentiality, the data collection questionnaire used by each database, outputs from the database, and information about the management of the database.

The full version of the DoCDat resource is still available through the NHS Information Centre here.

Cancer registration in developing countries: luxury or necessity?

This is the title of an article in the Lancet Oncology - free to read after registration due to the nature of the topic: linked here

There are several benefits which may accrue to developed nations who are willing to help with the process and technology of registration in the developing world - facilitating the conduct of clinical trials has multiple benefits including helping developed nations better treat their citizens whose immediate parentage links them to developing nations - observations made on significantly larger populations sizes than may be available in the developed nations can lead to better tailored treatment for those of e.g. East African origin living in e.g. the United Kingdom.

This is why we have been working recently with the International Network for Cancer Treatment and Research (INCTR) to develop resources which will benefit those working in cancer control in the developing world.

Thanks to the INCTR for tweeting this article - retweeted by us - see recent tweets!

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