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.
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.”
The Garvan Institute of Medical Research has signed a memorandum of understanding with Genomics England, the organisation established by the UK’s Department of Health to deliver the world-first 100,000 Genomes Project. The two organisations will share resources and expertise to advance genomic medicine in Australia and the UK.
Professor Mark Caulfield, Genomics England and Professor Marcel Dinger, Kinghorn Centre for Clinical Genomics at Garvan.
The 100,000 Genomes Project will sequence genomes from around 70,000 National Health Service (NHS) patients, focusing on individuals with rare diseases or cancer. Through the project, Genomics England aims to bring benefit to patients, build capability in the burgeoning area of genomic medicine, and advance medical research.
Under the terms of the agreement, Garvan and Genomics England will work together to make genomic information more accessible, meaningful and usable, particularly by developing better ways to capture clinical information and integrate it with genomic data.
In addition, the two institutions will collaborate to develop next-generation genomics databases and to establish clear ethical and legal frameworks around the use of genomic information. They will also collaborate to design educational resources about clinical genomics for health professionals and the wider public.
Professor John Mattick, Executive Director of Garvan, says that partnering with Genomics England is an important step in the development of Australia’s genomics capacity.
Professor Mattick says, “This agreement is an important step for both nations. It enables us to use our complementary expertise to advance our shared vision of the global transformation of medicine through the use of genomic information.”
Professor Mark Caulfield, Chief Scientist at Genomics England, says, “I am delighted we are collaborating with the Garvan Institute of Medical Research in Australia. This partnership will allow us to share tools and approaches to harmonise datasets in Australia and the UK. Our aim is to support other countries in establishing similar programmes to the 100,000 Genomes Project around the world.”
As one of Australia’s leading medical research institutions, Garvan develops research programs that combine leading-edge science with clinical outcomes. In 2012, Garvan established the Kinghorn Centre for Clinical Genomics (KCCG), the largest sequencing centre in the southern hemisphere. KCCG is undertaking research and developing innovative analytical pipelines to advance the use of whole-genome sequencing in clinical diagnosis and patient care.
Genomics England has developed a unique resource, the ‘PanelApp’. It is a new crowdsourcing tool for the scientific community, allowing knowledge of rare disease genetics to be shared and evaluated. This will create comprehensive evidence-based gene panels for rare diseases. The resource is publically available for anyone who would like to view and download the gene panels. Experts can register as a reviewer to make evaluations of the gene panels.
Dr Ellen McDonagh, Lead Scientific Curator at Genomics England said: “We’ve developed the PanelApp to crowd source knowledge of genetic testing for rare diseases and provide a tool for experts to utilise. We are encouraging those with an expertise in rare disease genetics to register to be a reviewer. We’d like experts to help finalise the list of genes that can be used to help diagnose a rare disease. The PanelApp also allows evidence for research grade genes to be collected, which may eventually be promoted to clinical grade as more evidence emerges. Currently gene panels differ from place to place; PanelApp is an opportunity to encourage standardisation of gene panels throughout the scientific community, based on expert knowledge and guidelines.”
The 100,000 Genomes Project is recruiting patients with 122 different rare diseases. For these patients the underlying genetic cause of their rare disease is not known, or is not certain. By looking at a person’s genome it is hoped that the likely genetic change that is causing their rare disease will be identified, and that they will be provided a diagnosis for the first time. In some cases this will help guide treatment to slow or halt progression of the disease.
There are millions of genetic variations between people. To help identify the genetic change that may be causing a rare disease, genome analysts use a variety of tools and techniques to narrow their search. One of these tools is a list of genes known to be involved in the rare disease. This separates the genetic changes in these genes from the rest of the genome, as they may be more likely to cause the disease.
For each rare disease that is a part of the 100,000 Genomes Project, a list of potential genes for each condition has been gathered – a gene panel. Four publicly available resources were used to create the panels. The role of some genes is understood and the effects they have on cells and the body has been discovered. Some of these genes are already tested for by the NHS to diagnose disease. For other genes, their function is less clear. Expert reviewers are being asked to assess the panels and provide evidence that a specific gene is involved in the disease.
Reviewers are asked to give each gene a rating on a scale of green = high evidence i.e. the gene is very likely be the cause of the disease and can be reported back to patients, to red = low evidence for a role in disease, or not suitable for clinical diagnosis at this time. Their ratings can be based on clinical or research-acquired knowledge. Reviews will then be consolidated based upon criteria established by Genomics England. Experts can also add new genes to the panel, and it is expected that the gene panels will be updated as we learn from the 100,000 Genomes Project data.
The wider clinical and scientific community are able to access and review the panels, and over time this will improve understanding of diseases.
Visit the PanelApp, or view the videos for a guide and demonstration.
The 100,000 Genomes Project had an exhibition stand at the UK’s major health and care conference, NHS Expo. The stand brought together key partners working on this ground-breaking project: Genomics England, Department of Health, NHS England and Health Education England. We also shared the stand with illumina, Congenica and WuXi NextCODE – innovative companies providing genome sequencing and genome interpretation for the Project.
Delegates came to visit our shared exhibition stand to learn more about genomics, including how DNA is sequenced, what happens with the results, and how these are interpreted.
Secretary of State for Health Jeremy Hunt visiting the stand
Attendees could extract their own DNA with help from colleagues from Manchester NHS Genomic Medicine Centre. Visitors can also follow the entire ‘journey’ each participant in the Project makes – from giving their consent to take part, to having their whole genome sequenced and the crucial annotation and interpretation of that data which leads to the feedback they eventually receive from their clinician.
We welcomed several VIPs to the stand. Secretary of State for Health Jeremy Hunt, Minister for Life Sciences George Freeman, Sir Malcolm Grant, Chair of NHS England, and Dame Una O’Brien, Permanent Secretary at the Department of Health were among the visitors.
DNA Extraction Demo
Professor Bill Newman, who is leading on the 100,000 Genomes Project at the Manchester Centre for Genomic Medicine (MCGM) said: “Saint Mary’s Hospital and The University of Manchester are delighted, in collaboration with other colleagues in Greater Manchester, to play a leading part in the 100,000 Genomes Project and the opportunity it presents to bring the latest genomic medicine to patients in our area.”
“Our stand at NHS Expo is just one part of our strategy developed by the Public Programmes Team at Central Manchester University Hospitals to engage the public with genomic science, and will show how we do that. People will be able to extract their own DNA from their cells – a fascinating process. ”
Check out our Storify for a roundup of tweets from the event.