Genomics England has selected Cognizant as a technology partner to help design and implement the IT operating environment for the 100,000 Genomes Project.
The 100,000 Genomes Project aims to sequence 100,000 whole genomes from NHS patients and their families, of which around 70,000 are participants with certain types of cancer or rare diseases. The project aims to enable new scientific discovery, medical insights and diagnostics. When completed, the NHS will be able to offer genomic medicine and personalised treatments to patients with conditions that are currently hard to treat.
As part of a two-year agreement, Cognizant will help provide end-to-end systems integration and analytics services for the technology platform built by Genomics England. This will enable Genomics England to augment its capability and capacity to process samples and interpret findings. An improved technology backbone supported by advanced analytics will also help Genomics England optimise its business processes and simplify the management and analysis of clinical, laboratory and health data.
“Combining genomic sequence data with medical records is a ground-breaking initiative. Researchers will study how best to use genomics in healthcare and interpret the data to help patients,” said David Brown, Head of Informatics Infrastructure, Genomics England. “We selected Cognizant for its extensive life sciences capabilities, knowledge of research, management and analysis of clinical data sets, and experience in working with the UK public sector organisations.”
“Large-scale sequencing initiatives like the UK’s 100,000 Genomes Project require a flexible, secure operating platform to help drive innovation in new diagnostic and treatment options for patients and healthcare providers,” said Bhaskar Sambasivan, Vice President of Cognizant’s Life Sciences practice. “Our culture of investing in understanding our customers’ businesses, deep programme management expertise in the healthcare and life sciences industry, and robust system integration and business analytics capabilities enable us to deliver a broad range of solutions for Genomics England as it creates genome sequences and clinical data at an unprecedented scale.”
Health Minister in the Northern Ireland Executive, Simon Hamilton, today announced £3.3m investment to create a Northern Ireland Genomic Medicine Centre that will provide rare disease patients with a much earlier and more accurate diagnosis.
It is estimated that 1 in 17 people are born with or develop a rare disease during their lifetime. At least 80% of rare diseases have an identified genetic component, with 50% of new cases being found in children. This investment will lessen the uncertainty and anxiety associated with not having a diagnosis for patients and their families, enabling the faster provision of appropriate treatment and care when a diagnosis is made.
The ongoing treatment and care of cancer patients, taking part in this programme, will be informed by information about their own genome. Improved treatment for future patients with cancer is also expected to increase as a result of this initiative.
Mr Hamilton said; “The creation of the NIGMC is one of the first actions in the Northern Ireland Rare Diseases Implementation Plan that I have launched today with an additional commitment of £70,000 investment to progress other key actions in the Plan.
“The Plan embodies my commitment to implement the UK Rare Diseases Strategy in Northern Ireland. It provides a holistic approach to caring for people with a rare disease and to maximise the available resources for research, innovation and collaboration across the UK to benefit the entire rare disease community. The Plan also provides the opportunity to work with the Republic of Ireland to realise the mutual benefits of cross-border collaboration on rare diseases.
“The NI GMC will bring together health, academia, industry and patients placing Northern Ireland, as part of the UK GMC network, at the forefront of medical innovation by sequencing genomes on an unprecedented scale, bringing better treatments to patients with cancer and rare disease.
“I welcome this partnership with NHS England, Genomics England Limited and the contribution of £750,000 funding for the NI GMC from the UK Medical Research Council. The Northern Ireland Executive is providing the remaining £2.5million investment in the GMC.”
Dr Nathan Richardson, head of molecular and cellular medicine at the Medical Research Council, said: “This is an exciting opportunity to establish a strong partnership between Northern Ireland and England in genomic medicine. These joint investments will help establish a centre of excellence in genomic medicine in Northern Ireland and will support the UK-wide ambitions to reap the benefits for patients from whole genome sequencing research and linkage to NHS data.”
Dr Shane McKee, chair of the NI GMC leadership group, said: “We are excited and delighted to be part of this important initiative. We welcome the Minister’s commitment to ensuring that our patients can benefit from – and participate in – the scientific advances that are coming directly from research into genes and genomes. In Northern Ireland we have a proven track record in rare disease and cancer diagnostics, and we already lead the UK in delivering vital health information to the point of care. Now the challenge is to turn clinical and genetic information into improved treatment and management.
Our participation in the 100,000 Genomes Initiative via the NI Genomic Medicine Centre will allow us to rapidly set up an infrastructure to deliver on these goals. The challenge will be to build an enduring legacy where patients, families, health professionals and researchers can create personalised precision care pathways that improve lives, enhance research, and support the wider community.”
Christine Collins, chair of the NI Rare Diseases Partnership said: “The Northern Ireland Rare Disease Partnership welcomes the publication of Northern Ireland’s Rare Disease Plan. The plan for the foundation of a Genomics Medicine Centre here in NI is especially exciting.
“The Centre brings hope and an opportunity to participate in building a better future for all families living with a rare disease; a superb new resource for the clinicians working to give them a diagnosis and improve understanding of their conditions; and clarity and impetus for those working to create new pathways for treatment and management.
“Northern Ireland has so much to contribute, as well as so much to gain, from these developments. Working together, we can reap the full benefits from these initiatives; and provide better opportunities for all our young people and families into the future.”
Professor Mark Caulfield, Chief Scientist of Genomics England said; “I am absolutely delighted that Northern Ireland are the first devolved nation to join the 100,000 Genomes Project. This funding by the NI administration and the MRC opens the opportunity of equity of access to genomic medicine for people across the province with rare disease, cancer and infection.”
Read more in the Department of Health, Social Services and Public Safety’s news story.
Genomics England selects LabKey Software for integrated data management solution
Genomics England has chosen the LabKey Server open source platform to provide its integrated data management solution. Genomics England will work with LabKey to design and develop a solution that will integrate and securely share complex clinical and genomic data for the 100,000 Genomes Project.
The 100,000 Genomes Project aims to sequence 100,000 whole genomes from approximately 70,000 people. Participants are NHS patients in the UK with certain types of cancer or with rare disease, as well as their families. The initiative will bring together an unprecedented depth of clinical and genomic information to improve prediction and prevention of disease, spur the development of new diagnostics, and support personalisation of medical treatments based on genotypes. This is currently the largest national sequencing project of its kind in the world.
The LabKey solution will facilitate aggregation, review and integration of phenotype and genotype information across contributing labs, clinical sites and repositories. It will also enable review, reporting and analysis of this information by both clinicians and researchers, ensure protection of patient privacy, and support data de-identification and knowledge sharing.
Jim Davies, Chief Technology Officer of Genomics England explains, “By partnering with LabKey, we bring on board an excellent software platform and a technical team whose expertise in developing enterprise solutions for biomedical research and healthcare will significantly accelerate our efforts.
“We are excited to build on the rich foundation of LabKey Server. It is unique among tools in this field for its quality, extensibility, and reporting and analytical capabilities.”
“We see enormous potential for the work of Genomics England to benefit both patient care and research. We are proud and excited to be part of this innovative initiative,” adds Michael Gersch, CEO of LabKey Software.
“Building on the LabKey Server platform lets Genomics England leverage years of development with hundreds of research institutions and focus investment on incremental functionality needed beyond this proven base.”
We have now sequenced over 5,000 whole genomes from patients and their families. These are largely from our pilot study for which we owe enormous thanks to NIHR Bioresource for Rare Disease, Cancer Research UK and Biomedical Research Centres across the country. The 100,000 Genomes Project is picking up pace. All 11 NHS Genomic Medicine Centres are up and running and recruiting patients for rare disease. A number of additional families are due to join the Project from the NIHR Bioresource Rare Disease programme and several GMCs are now recruiting cancer patients as well.
Histopathologist marking up a tumour sample slide for whole genome sequencing.
Dr Anna Schuh, Director of the Oxford NHS Genomic Medicine Centre said: “For some of these patients, this new diagnostic approach will alter clinical management and can guide clinicians towards more effective treatment options. At the same time, by helping to recruit thousands of patients to this unique programme across England, we will make a significant contribution to collaborative research aimed at improving our understanding of these diseases which will ultimately lead to successful design of new therapies.”
As we reported in our last update, collecting DNA for sequencing from cancer biopsies has presented us with challenges. We are evaluating the different elements of sample handling and processing to optimise the quality and quantity of DNA for sequencing. One of the main areas we are looking at is different DNA preparation methods – using freshly frozen samples versus samples preserved using the ‘FFPE’ (formalin fixed, paraffin embedded) method. FFPE processing is more routine in cancer diagnosis in the NHS, but the process affects the quality of the DNA. The fresh frozen method gives better quality DNA, but is not suitable for every tumour type, and not always practical.
We are working through these challenges with research collaborators, partners in pathology services and NHS England. The issues are not unique, and so our work will help inform other clinical and research studies in the NHS too. Our aim is to drive up quality of cancer DNA samples for molecular testing in the NHS, which will serve this programme but also have positive impact in delivery of cancer testing in the NHS more broadly. The results of our experiments will be back later in the year and will be used to improve the methods we use in the Project and beyond.
Support your professional development by enrolling on one of the ground-breaking HEE-funded genomics courses.
The Genomics Education Programme (GEP) is the NHS’s method of ensuring its staff have the knowledge, skills and experience to ensure that the health service remains a world leader in genomic and precision medicine – particularly for NHS England Genomic Medicine Centres (GMCs) and their contribution to the 100,000 Genomes Project.
The Master’s in Genomic Medicine and individual CPPD modules have been developed to provide a multi-disciplinary and multi-professional course in genomics that can be applied to clinical practice and medical research. The Master’s or individual CPPD modules will enhance knowledge and skills in this rapidly evolving field.
The course itself will cover the following topics:
Introduction to human genetics and genomics
Genomics of common and rare inherited disease
Molecular pathology of cancer and application in diagnosis, screening and treatment
Pharmacogenomics and stratified healthcare
Application of genomics in infectious disease
Interested candidates can apply for the one year full-time, or a two year part-time Masters, or, if time or resource is limited, individual modules can be taken as CPPD. The GEP is funding more than 500 Master’s places across the clinical professions together with 1000 individual modules for CPPD.
The Master’s programme and individual CPPD modules are being delivered by a national network of nine universities covering England. If you are interested in completing either the Masters or individual CPPD modules please check your favoured university to obtain details of the programme modules, entry criteria and timing before going through the funding application process.
For more information about participating Universities, the Genomics Education Programme and our other free resources please visit: http://www.genomicseducation.hee.nhs.uk/
Further information about the funding application process is available here:http://www.genomicseducation.hee.nhs.uk/msc-funding-form/
The Health Education England Genomics Education Programme (GEP) is offering NHS professionals fully-funded continuing personal and professional development (CPPD) modules as part of its work to ensure the health service remains a world leader in genomic and precision medicine.
These Masters-level modules have been developed as part of a multi-disciplinary and multi-professional course in genomics that can be applied to both clinical practice and medical research. They will allow professionals to enhance their knowledge and skills in this rapidly evolving field.
There are 16 different modules available covering the whole range of genomic medicine. These include:
Introduction to human genetics and genomics
Genomics of common and rare inherited disease
Molecular pathology of cancer
Ethical, Social and Legal issues
The modules are open to the full range of clinical professions and NHS managers and credits from individual modules can be built up into a Postgraduate Certificate or Postgraduate Diploma.
The courses are being delivered by a national network of nine universities across England. More details of the modules, eligibility criteria and how to apply are available on the Genomics Education Programme website.
We are delighted to be working with Roald Dahl’s Marvellous Children’s Charity and researchers based at Great Ormond Street Hospital (GOSH) to help create a new role to support children and young people with undiagnosed genetic conditions and their families.
To celebrate the launch of the Trust’s involvement in the project and to commence patient recruitment at Northwick Park Hospital, a series of talks and presentations were given to Mayors, local councillors, representatives from the Department of Health, NHS England, GPs, patients and staff, on the benefits of genomic medicine.
Genomics England has today (30th September 2015) announced that it has contracted with Congenica and Omicia to work with them on the interpretation of the genomes from 8,000 patients participating in the 100,000 Genomes Project. Work with LockheedMartin-Cypher, Nanthealth and WuxiNextcode continues as part of a test phase. This is in addition to ongoing work with sequencing partner Illumina who are also exploring a variety of bioinformatic challenges around sequencing and clinical interpretation.
Genomics England is also announcing that two new companies, Berg Health and NGM Biopharmaceuticals have joined Genomics England’s industry collaboration, known as the GENE Consortium. BERG is a Boston based biopharmaceutical company and NGM Biopharmaceuticals is based in South San Francisco. Both will join the other members of the GENE Consortium who are already working on a year long industry trial assessing how best to engage with Genomics England to accelerate the development of new diagnostics and treatments for patients.
GENE Consortium discussion
Sir John Chisholm, Executive Chairman of Genomics England said;
“We are delighted to welcome two new partners to the GENE Consortium. Exploring how industry will work with this unique dataset along with driving up the quality of the interpretation of genomic data are crucial to us in finding out how to understand and treat disease better in the future. It’s this that will ensure genomic medicine benefits patients for years to come.”