IDBS Data Management Blog

Big Data is a Big Topic, fuelled by the impact of low cost genomic sequencing, adoption of electronic medical records and growth in personalized medicine approaches. From research to the clinic, translational medicine depends on properly integrated, managed and analyzed high quality data. This was the theme for the 4^th annual IDBS Translational Medicine Symposium on Tuesday December 11th.

Held in central London at the prestigious Dorchester Hotel, nearly 90 attendees came to hear the latest news and developments in translational medicine in the UK. It was a packed day with eight speakers plus IDBS CEO Neil Kipling, contributing to a very focused discussion on what IDBS are doing to support this exciting field.

The announcement of a £100m DNA database provided the back drop to look at how capture, management and analysis of data and its context is critical to success in science. Sound familiar? Anyone who has worked with IDBS or has worked in life sciences knows that this is who we are. IDBS is about data. This is why data was selected as the theme of the event. Big Data is a hot topic and many groups are trying to make use of sparsely populated and poor quality patient records – something we know a lot about, and this came through strongly in the presentations.

Speaker highlights included:

• Neil Kipling explained why IDBS is in the translational space and how this is a very personal crusade for him to make a difference to patient treatment and outcomes
• Nick Craddock from the Wales National Center for Mental Health explained how IDBS is supporting a 6,000 person prospective study into mental disorders such as ADHD, Schizophrenia and Biopolar disorder
• Jim McGurk from Daiichi Sankyo highlighted why even well populated clinical trials datasets are hard to integrate, and described an IDBS project to do just that across 17 clinical studies
• Jon Green from the Health Protection Agency described how Next Generation Sequencing is used to analyze bacterial strain outbreaks, such as E.coli, and how he is looking forward to working with IDBS on this
• Robin Munro presented our vision of how Big Data in healthcare can be managed, with a particular emphasis on how E-WorkBook can be used with genetic datasets to improve collaboration
• Mike Barnes covered a long and challenging project at Bart’s Health that he has completed with IDBS to integrate clinical data sets in cardiovascular disease
• Julie Barnes explained how the 200,000 person UKCTOX project on endometrial cancer has developed a great resource for biomarker development at Abcodia, which uses IDBS software for cohort analysis
• Will Spooner from Eagle Genomics talked about end-to-end data management in Next Generation Sequencing
• Yike Guo closed the day with his usual tour de force of Big Data in life sciences and described the E-TRIKS project

Finally, one of the most encouraging comments I heard was from a team at Imperial College. They observed how all the speakers discussed IDBS becoming a part of their project teams, part of the family in many ways, and shared that they got the impression we were a great company to work with because of our commitment to our customers success. This commitment to customer success comes from the top, from Neil Kipling, and makes IDBS who we are. This is what we stand for; excellence in data and in our people.

The recent news of an NHS driven DNA database for 100,000 subjects in the UK is a major statement of intent from the government. Following up on announcements regarding access to patient data via the Clinical Practice Research Database (CPRD) and calls for the NHS to lead the world in genetic medicine last year, this is a further step towards improving patient care with better knowledge of our genomic characteristics.

With 60 million people under one health provider, the NHS has the capacity to curate world-leading data and insight into the best patient treatments and associated genetic characteristics. If successful, this will also be a highly valuable resource to attract drug companies to perform precision clinical trials and studies in the UK, and provide invaluable patient data to newcomers in the market such as nutriceuticals, health app designers and food & drink producers. This resource could drive an ecosystem of small & medium enterprise (SME) and start-ups to build health-based products built on a detailed understanding of patient population and individual subject characteristics.

Key to the success of the project will be:

• Quality of the clinical and genomic data that is collected and stored
• Reproducibility and accuracy of genomic sequencing
• Data analysis and presentation to support research and clinical decision-making, which is critical to ensuring the information is usable by different communities

Genomic sequencing techniques are still rapidly evolving, resulting in challenges in preparing samples for analysis and in consistent data analysis. Having a single/small number of sites will help this tremendously, but end to end data management (from sample to report) is key to reproducibility, audit trails and data provenance.

The ability to stratify patient populations enables pharma companies to run smaller, more efficacious trials because the predicted outcome is so much more impactful. Profiling large patient populations for clinical characteristics and molecular markers will be a huge benefit to pharma and UK-based trials, allowing populations to be stratified to a strong responding set of target patients, which will often be smaller than a standard trial.

£100m shows a strong commitment to create a knowledge resource to be reckoned with, although realistically this budget will quickly be eaten up over the course of five years.

IDBS is supporting this field in a number of major UK hospitals, many of whom recently spoke at the IDBS Translational Medicine Symposium in London. Quality of clinical data, standardization of genetic analysis and challenges in combining clinical and genomic data were all key topics.

A new collaborative data environment that will transform the world

There’s nothing quite like the morning after a good party. It’s a rollercoaster of reflection, recovery and sometimes embarrassment. It’s also often a time of new resolutions. For many of us the New Year provides the biggest ‘morning after the night before’ than most. Our article in yesterday’s  Genetic Engineering& Biotechnology News talks about the morning after the 50 year party enjoyed by the Life Sciences who are waking up to a new world. This world has important new stakeholders, such as patients, it’s more globalized and collaborative. There is payerpower, patient power and new science that is helping to drive the change and it’s demanding action. Translational medicine, personalized medicine, precision medicine, call it what you will, the Life Sciences are now focussed on outcomes and on delivering treatments that fit the disease like never before. Above all it is data driven.

Improve the data quality, improve the decision.

So is all this just Big Data? No. It’s about deep insights into what data need to be collected and smart (not just big) systems that make the data usable, then taking informed action to change practise for the better.

It is well established in Life Sciences and clinical environments that there remain significant gaps in data which make data comparisons, big or not, of limited value. Our work across industry and healthcare environments drives changes in clinical and R&D practise that address the data gaps and focus upon getting collaboration to work across these multiple disciplines. This was put well by Dr James McGurk when he said at IDBS’ Translational Medicine Symposium in London: “The more difficult it is for others to understand your data, the more likely it will be used badly.”

Welcome to a Big New Year!

The battle has long raged over the impact of nature (in the form of genetics) vs Nurture (in the form of environmental factors) on an individual’s susceptibility to disease. Clearly both play a huge part in deciding the expressed phenotype, but scientists always struggled to explain the variation in phenotype found between identical genomes even in the same lab conditions or between twins raised in the same household.

The reason for these variations may well be due to the unknown purpose of large sections of DNA previously believed to be ‘Junk’ (also known as Dark Matter). New research shows that 80% of the genome is now biologically relevant as opposed to the 2% of protein coding genes that were previously the regions focussed on.

These findings were identified by the Encode project (The Encyclopaedia of DNA Elements), which recently published 30 connected open access journal papers based on the work of 400 scientists from 32 labs in the UK, US, Spain, Singapore and Japan. Started 5 years ago the project has cost $288 million and was set up to explain the findings of the 2003 Human Genome Project, which highlighted only 2% of genes were involved in producing blood, bone and tissues. The work was based on more than 1600 experiments and 180 different cell types.

The project identified four million gene ‘switches’ or regulatory genes, which are areas of DNA that control when genes are turned on and off in a cell and hence how much of any particular protein is produced. It was of particular interest that these switches were often not located close to the gene encoding regions of DNA, explaining the assumption that these other regions were Junk. This had been questioned for some time has and now been proved incorrect.

It seems regulatory genes are of significance for rare diseases, such as Crohn’s disease, as well as more common diseases such as cancer. Considerable early excitement surrounded mistakes in single gene or monogenic disease such as sicklecell anaemia, but the complexity of human biology has proved that the majority of disease is polygenic. The impact of mistakes in regulatory genes is much more significant and is suspected to be 5-10 times more impactful than mistakes in coding genes. For example, cancer defects in 20 regulatory genes surface repeatedly in 17 major cancer types, providing new avenues for drug targets and personalized treatments.

Use of these new findings in medical treatment is still a long way off. This project demonstrates why basic, fundamental research is key to understanding the building blocks of life. As we continue our journey into the mysteries of human existence and disease susceptibility, the incredible foundation of our lives that is DNA continues to amaze us with its sophistication and complexity.

Friday January 20, 2012 was a proud day for the Healthcare team at IDBS as our new US Healthcare Center of Excellence was opened by Massachusetts Governor Deval Patrick in front of a crowd of local dignitaries, press and analysts, customers and, of course, our employees.

New gene sequencing technologies have – in the space of only 12 years – reduced the cost of sequencing a human genome from $3bn to $1000. To apply this data to clinical decision support requires new approaches to data management and understanding of genetics in the clinic. Our translational medicine solutions provide an enabling capability.

We see tremendous opportunity for Massachusetts and the rest of North America, as a result of the Meaningful Use Program, to advance scientifically and clinically from the growing availability of electronic medical records, but clinical and genetic data needs to be pulled together and made consumable by those who can take action for the benefit of patients.

Forward-looking organizations we speak with are looking for ways to use data from the clinic to accelerate research and then to apply the genetic and genomic understanding back into the clinic. With our ground breaking new systems, such as the ORIS project at King’s Health Partners, we are delivering this critical piece of the personalized medicine puzzle.

We believe it is critical to unite diagnostics, pharmaceutical, academic centers and now hospital environments to create a collaborative genomically-centered ecosystem that is focused on improving patient care and research. Our new Center of Excellence is the hub around which we are building these systems in the US.