Month: February 2016

Rare Disease Day 2016

Our clinical lead for rare disease, Dr Richard Scott, gives an update on our work. February 29th 2016 is Rare Disease Day.

Rare disease is a deceptive term. There are 6,000 to 8,000 different rare diseases. This means that although each one is rare, as a group they are common. So much so, that 1 person in 17 is affected with a rare disease. That is 7%.

Until recently, these usually complex and long term diseases have been the second class citizens of the medical world. But now there is an increasing focus on them. It has been a long time coming. For years, people suffering with rare diseases have struggled to be diagnosed, let alone have access to the same expert medical advice and tailored treatment plans that have become the norm for many common long term disorders such as diabetes and heart disease.

Rare Disease Day logoThe change has come thanks in large part to ‘patient power’ – witness today’s celebration of Rare Disease Day, the brainchild of the Rare Disease patient advocacy group EURODIS, to raise awareness of rare disease. Since its launch in 2008 it has spread to more than 80 countries.

In parallel, strategic responses to the unmet needs of rare diseases have been forthcoming. In the UK, publication of a National Strategy for Rare Disease in November 2013 has been part of the response. Today, an update from the UK Rare Disease Forum has been published, showing progress so far and what work is still to be done. The government also funded our ground-breaking 100,000 Genomes Project, which aims to transform healthcare for people with rare disease and cancer.

About 80% of rare diseases have a genetic cause. The cause is often a single changed ‘letter’ amongst the 3.2 billion letters of DNA that make up the human genome. Finding that one crucial change is often like finding a needle in a haystack. This first crucial step – identifying the cause of the disease – has remained challenging until now for most rare diseases. In turn, this has prevented medicine from answering the obvious next questions for rare disease patients: what should I expect in the future? Why has the disease happened? Is there a way of curing my disease or any hope of doing so in the future? Will my child have the disease?

The 100,000 Genomes Project is an opportunity to break the mould for patients in the NHS. We will sequence DNA from patients with rare disease and their relatives. By comparing their sequences with people without the disease and by tracking the inheritance of DNA changes through families, we can find the cause in people who medicine has failed to diagnose until now.

No-one has ever attempted whole genome sequencing on this scale before. Much of our work until now has been in establishing the tools and infrastructure we need to deliver results to 100s of participants a week.

Thirteen ‘NHS Genomic Medicine Centres’ have been commissioned to act as recruitment hubs, each with a network of local recruiting hospitals. Here, participants are identified and consented by local clinical teams and DNA samples and standardised medical data collected. The sequencing itself is performed in a purpose-built facility near Cambridge before the genome sequences are analysed alongside the medical data in a secure, monitored data centre.

The scale of the task is only possible because of the great power of the new sequencing technologies and computing. As Spiderman tells us ‘with great power comes great responsibility’ and it is with this sense of responsibility that we approach the work: both driving us to capture every ounce of available expertise and to exert the necessary caution when patient’s lives are influenced by the outcome of our analysis.

The Project bioinformatics team have established the core analysis ‘pipeline’, which is further enhanced by the input of genome annotation partner companies. This analysis infrastructure is supplemented by the expertise drawn from a collaboration of more than 2,000 academic researchers from across the UK and the world who form the ‘Genomics England Clinical Interpretation Partnership’ (GeCIP for short) and from the clinicians at the recruiting hospitals as they receive the sequence results and return them to the participants.

But the aims of the project do not end at interpretation of genome data for diagnosis. The GeCIP research community seeks also to understand the processes that lead to the diseases and to develop precision medicine approaches to their treatment. To enhance the speed with which potential treatment benefits can reach patients, we have established a unique partnership between our academic and NHS partners and companies from pharma, biotech and diagnostics. Through this collaboration, we are developing approaches that will reduce the length of time from the first identification of a cause of a condition to the development of life changing treatments.

We are already making our first diagnoses for families enrolled in the study. We hope that this will become commonplace and that the benefits won’t stop there, instead it will become the expectation of rare disease patients to receive the same standard of care and access to precision medicines as for common diseases.

This post also appears on the Huffington Post Tech blog.

Genomics England Enters Bioinformatics Partnership with Illumina

illuminaGenomics England and Illumina, Inc today announce a partnership to develop a platform and knowledge base that can be used to improve and automate genome interpretation. The tools will operate within the Genomics England secure database to enable researchers and clinicians to access information and reports more readily.

Genomics England is partnering with Illumina to develop and deliver systems for clinical interpretation, decision support and knowledge curation for the 100,000 Genomes Project. This non-exclusive partnership with Illumina will run in parallel with the other clinical interpretation and bioinformatics providers involved in the 100,000 Genomes Project.

Illumina and Genomics England will collaborate to develop a set of informatics tools, which will support the delivery of genomic clinical and research services at a population scale to the NHS Genomic Medicine Centers and the Genomics England Clinical Interpretation Partners. All of the tools will include open application programming interfaces so that other bioinformatics solution partners can continue to provide services within the Project.

Under the terms of the partnership, Illumina will develop interpretation and reporting tools for the purpose of delivering reports on all genomes that are sequenced through the 100,000 Genomes Project. Genomics England will provide access to whole genome sequence and de-identified phenotypic data for the development of this suite of tools for personalised medicine. The tools will be used to curate and manage the knowledge base of information generated over the course of the project with a focus on rare disease and common cancers. Illumina and Genomics England have agreed to make available the clinical findings arising from the 100,000 Genomes Project to approved users of the tools developed through the collaboration.

The partnership also includes the ability for Genomics England to work with Illumina’s other tools, NextBio® and BaseSpace®, for data access and genomic data management. Illumina will make available to Genomics England researchers and the GENE Consortium part of the 100,000 Genomes dataset as a pilot within NextBio® Clinical, which will enable cohort analysis of complex phenotypic and genotypic information from de-identified genomes.

We are both committed to patients benefiting from genomic analysis across the NHS and to supporting clinicians and researchers in finding new genomic insights

“Our partnership with Genomics England will help change the way healthcare is practised” said Jay Flatley, Illumina’s Chief Executive Officer. “The development of our suite of technologies and platforms is critical to enabling physicians in the future to make educated diagnoses based on a patient’s genome which will lead to better health outcomes.”

Sir John Chisholm, Executive Chairman of Genomics England said: “This agreement allows Genomics England to access Illumina’s bioinformatics knowledge and experience to support our ambitions of transforming patient care and research. We are both committed to patients benefiting from genomic analysis across the NHS and to supporting clinicians and researchers in finding new genomic insights. Illumina is our key sequencing partner and they are now able to also support us, alongside our other partners, in solving the challenges of delivering clinical reporting and knowledge curation at a national scale”

More information

Sequencing partnership with Illumina

This agreement is an extension to our sequencing partnership with Illumina, which was announced in August 2014. Illumina remain our sequencing partner for the 100,000 Genomes Project.

The new bioinformatics partnership will develop a set of informatics tools, which will support the delivery of genomic clinical and research services at a population scale to the NHS Genomic Medicine Centres and the Genomics England Clinical Interpretation Partners.

The bioinformatics partnership is a non-exclusive partnership between Genomics England and Illumina which will run in parallel with the other clinical interpretation and bioinformatics providers involved in the 100,000 Genomes Project. All of the tools will include open application programming interfaces so that other bioinformatics-solution partners can continue to provide services within the Project.

Other bioinformatics partners

Last year we announced our contracts with Congenica, Omicia, Nanthealth and WuxiNextcode. These companies are also providing clinical interpretation services in the 100,000 Genomes Project.

We will continue to work with a range of partners. We expect the work with a variety of companies will complement each other, helping us to provide the best possible interpretation of genomic data. We will always look to work with companies who can provide the right expertise across a wide range of bioinformatics challenges.

Genomics England selects ICON as Data Management Partner

icon-logoGenomics England has today (09/02/16) announced that it has selected ICON plc, a global provider of drug development solutions and services to the pharmaceutical, biotechnology and medical device industries, as data management partner for the 100,000 Genomes Project.

ICON will use its genomics expertise and powerful data management capabilities to validate clinical data from the 70,000 participating patients and their families. This work will take place within the secure Genomics England data environment.

“We are very proud that our genomics knowledge and our capabilities in securely managing large clinical and real world datasets have been chosen by Genomics England for such an important and transformative project,” commented Professor Brendan Buckley, ICON’s Chief Medical Officer.

“Our partnership with Genomics England demonstrates our commitment to partnering with industry and government organisations in new and innovative ways to improve patient care by accelerating the development of targeted and personalised medicines that tackle complex diseases. Genomics England’s selection of ICON also reaffirms ICON as a trusted partner to government organisations as well as the world’s top pharma, biotech and medical device companies.”

James Peach, Managing Director for the 100,000 Genomes Project Main Programme at Genomics England said:

“We are delighted to be partnering with ICON. Their renowned expertise in data management will be fundamental in driving scientific research and accelerating the return of results for NHS patients”