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Genomics England selects LabKey Software for integrated data management solution

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.

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.

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.”

5,000 Whole Genome Sequences

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.

Maddison, aged 6, was the first patient recruited at University Hospital Southampton. Read her unique story and why her family took part in the University’s research newsletter. In Oxford, the first cancer patients were recently recruited. In total more than 1,200 patients and their families who are looked after by the Oxford University Hospitals NHS Foundation Trust will take part.

histopathologist marking up a tumour sample slide for whole genome sequencing

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.

Get ahead and Master your Genomic Knowledge

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
  • Bioinformatics interpretation

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:

Further information about the funding application process is available here:

Keep up with the latest developments in medicine with fully-funded Genomics CPPD Modules.

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
  • Advanced Bioinformatics

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.

Genomics England announces interpretation partners and expands industry engagement

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

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.”

Garvan partners with Genomics England to advance genomic medicine

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.

Mark and John

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.”

Garvan logoProfessor 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.

New rare disease gene tool launched – PanelApp

PanelAppGenomics 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.

 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

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.

Genomics at NHS Expo 2015

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

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

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.

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