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Genomics England and Inserm partnership strengthens UK-French cooperation in genomic medicine

As part of the UK-French summit held in Sandhurst yesterday (18 January 2018), the UK and French Governments have announced enhanced cooperation between Genomics England and the French ‘Médecine Génomique 2025’ project.

The Strategic Genomic Medicine Partnership marks a strengthening of the existing relationship between Genomics England and the French National Institute of Health and Medical Research (Inserm). Formalising the agreement, senior representatives of both organisations signed a letter of intent for a Memorandum of Understanding (MoU).

The UK and France will combine our shared national attributes by co-funding shared analysis of new technologies to accelerate genomic medicine and research collaboration, ultimately improving the care of patients with cancer and rare diseases.

L-R: Matt Hancock MP, Sir John Chisholm, Yves Levy and Brune Poirson, at the UK-France Summit 2018.

Genomics England Executive Chairman, Sir John Chisholm, said:
“The Strategic Partnership announced today sees two global pioneers combining know-how to realise the full potential of genomic medicine. Genomics England and Inserm will work together more closely than ever before – signalling our joint ambition to lead the world in genomic discovery, develop more effective treatments and drive economic growth in the sector.”

Genomics England Chief Scientist, Professor Mark Caulfield, said:
“Today’s agreement ensures that the UK and France continue to set the pace in global genomics. Both of our nations are on the verge of introducing genomic medicine into mainstream health services and this enhanced cooperation will allow us to set new and lasting global standards, share learning and, ultimately, deliver the best possible care to our patients.”

Genomics England adopts Edico Genome’s DRAGEN Bio-IT Platform

Genomics England adopts Edico Genome’s DRAGEN Bio-IT Platform to increase accuracy, consistency of next-generation sequencing analysis

Today (8 January 2018) at the annual J.P. Morgan Healthcare Conference, Edico Genome and Genomics England announced a new partnership to strengthen the accuracy and consistency of next-generation sequencing data analysis in Genomics England’s Rare Disease Pilot.

The partnership will further support Genomics England’s 2018 initiative to making next-generation sequencing (NGS) the standard of care across the UK’s National Health Service in 2018. Specifically, the partnership will focus on the analysis pipeline − improving alignment and variant calling in whole genome sequencing data. Genomics England selected DRAGEN for its industry leading accuracy and speed, enabling the organisation to accelerate analysis of large clinical genomic datasets.

“Working with Edico Genome, Genomics England moves one step closer to reaching genomic medicine’s full potential, and improving the efficiency of whole genome analysis to help diagnose rare diseases,” said Joanne Hackett, chief commercial officer at Genomics England. “This partnership demonstrates our commitment to harnessing the most innovative technologies in the world to maximise patient benefit.”

Genomics England is currently using DRAGEN to re-process 5,000 whole human genomes from individuals with rare diseases. These genomes were originally mapped and aligned on reference genome GRCh37, but an updated human reference genome has since been released, GRCh38, which offers increased accuracy and consistency of results. These reprocessed datasets will be provided to pharma and industry partners for additional analysis through the Discovery Forum, a platform for collaboration and engagement between Genomics England, industry partners, academia, the NHS, and the wider UK genomics landscape. In conjunction with the announcement, Edico Genome has joined Discovery Forum.

“Genomics England is truly paving the way for the widespread integration of whole-genome sequencing on a population scale, bringing the future of personalized medicine into the now for individuals across the U.K.,” said Pieter van Rooyen, Ph.D., president and chief executive officer at Edico Genome. “Our bioinformatics and engineering teams are committed to pushing the envelope in terms of accuracy, sensitivity, speeds and scalability to ensure the highest level of personalized care can be delivered in a timely, cost effective and economical manner. We are honored to be able to assist in such an important undertaking – helping diagnose rare diseases — and look forward to bringing further optimizations and new pipelines to customers in 2018.”

By leveraging field programmable gate arrays (FPGAs), DRAGEN provides outputs almost instantaneously and processes clinical grade genomic data at record-breaking speeds. To ensure precise results, all DRAGEN pipelines feature validated algorithms for enhanced accuracy. DRAGEN can be implemented onsite, in the Cloud, or through a blended hybrid-cloud solution.

Edico Genome

Genomics England appoints two new Non-Executive Directors to its Board – to build strategic, medical and commercial strength

Genomics England has announced the appointment of two new Non-Executive members to its Board. Sir Ron Kerr and Keith Stewart bring a wealth of senior scientific, commercial and managerial experience to Genomics England − providing effective support for the strategic and operational leadership of the organisation.

Genomics England’s new Non-Executive Directors bring highly relevant professional expertise and the ability to engage with stakeholders at every level. They are tasked to ensure the on-going pace, innovation and impact of Genomics England’s pioneering work, helping to plan for the future as it progresses beyond the 100,000 Genomes Project:

Sir Ron Kerr

  • Sir Ron Kerr is currently: a Special Adviser to the Board at Guy’s and St Thomas’ NHS Foundation Trust – with a particular focus on commercial issues; Non-Executive Chair of the Bristol, North Somerset and South Gloucestershire Sustainability and Transformation Partnership (STP); Member, Board of Trustees, University of Bristol; and Member, Board of Trustees of the Guy’s and St Thomas’ Charity. His career spans 40 years – including CEO at the National Care Standards Commission and senior leadership roles across the NHS. Sir Ron is married with three children and was knighted in 2011 for services to the NHS.

Keith Stewart

  • Keith Stewart brings an internationally recognised reputation as a leader in the field of genomics. He is currently: Professor of Medicine at the Mayo Clinic College of Medicine and Science (US); Consultant – Division of Hematology/Oncology, Department of Internal Medicine (Mayo Clinic); Vasek and Anna Maria Polak Professor of Cancer Research (Mayo Clinic); Carlson and Nelson Endowed Director – Center for Individualized Medicine (Mayo Clinic); and Consultant – Department of Clinical Genomics (Mayo Clinic). Keith brings a focus on the clinical applications of genomics, sits on a number of scientific advisory boards and has considerable interest in business development activities – setting up two biotech start-ups and holding a number of patents.

Genomics England Executive Chair, Sir John Chisholm, said:

“Sir Ron Kerr and Keith Stewart join Genomics England at a critical moment. Between them they bring deep experience − of the NHS, cutting-edge genomic medicine and commercial opportunity. Their appointment to the Genomics England Board gives us invaluable insight – both as the NHS is on the cusp of introducing the world’s first genomic medicine service and we work to make the UK the global centre of genomics research, innovation and investment.” 

Sir Ron Kerr said:

“As someone who believes fundamentally in the value and potential of the NHS, I am delighted to join Genomics England.  As a Non-Executive Director I hope I can provide some helpful insight and advice that will help to drive true transformation – harnessing that power of genomic medicine for the benefit of patients in the UK and around the world.”

Keith Stewart said:

“Genomics England is an acknowledged global leader in the field of genomic medicine and I am excited by its potential. I will use my experience in translating genomic medicine in the clinic to help this groundbreaking organisation develop and grow ¬– creating new opportunities for patients, the NHS and the UK economy.”

Genomics England welcomes the UK Life Sciences Sector Deal

In response to yesterday’s Life Sciences Sector Deal announcement from the UK government, Sir John Chisholm, Executive Chair of Genomics England said:

“I warmly welcome the UK Life Sciences Sector Deal announced on 6 December – and congratulate Sir John Bell and all of those who have created a transformative roadmap for Life Sciences in the UK.

From the outset, Genomics England has worked to translate the UK’s world leading genomic research into a vibrant UK genomics industry. The Life Sciences Sector Deal recognises and builds on the progress that Genomics England has made in aligning pioneering science with the needs of industry to make the UK the global centre of genomics research, discovery and investment.

The Life Sciences Sector Deal represents a bold ‘green light’ from Government – placing genomic discovery at the heart of the Life Sciences. We are committed to seizing this once in a generation opportunity – furthering our deep industry partnerships to help transform the NHS, bring benefit to patients and drive UK economic growth.”

View our Industry Partnerships pages

Alex’s Story

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In this video, meet participant Alexander Masterson and his mum, Kirsty, who speak about what getting a diagnosis from the 100,000 Genomes Project means to them.

Find out about the rare disease that he was diagnosed with as a child, Noonan syndrome, and how his recent genetic diagnosis of LEOPARD syndrome is changing their view.

Hear from Alex about his experiences of living with his rare disease, as well as his plans for the future.

Thank you to Alex and Kirsty for sharing their story.

Meet more participants

All NHS GMC Contacts | South London NHS GMC

Discovery Forum – partnership on an industrial scale

– by Joanne Hackett, Genomics England Chief Commercial Officer

Genomics – on an industrial scale

The time for talking about the potential of genomic medicine is past. As England’s Chief Medical Officer (CMO), Dame Sally Davies, writes in her report, Generation Genome: “Genomics is not tomorrow. It’s here today.”

Genomics will transform patient outcomes and healthcare systems – and NHS England is already moving to make a mainstream genomics medicine service a reality. Realising this potential fully, however, demands more. As the CMO notes, we need to make the leap from genomic medicine as a “cottage industry”’ to genomic medicine on an industrial scale. It may sound obvious, but this transformation can only take place with deep industry partnerships in place.

Kick-starting a UK genomics industry has been a core Genomics England aim from the outset. It recognises that − while NHS England, Genomics England and others build the data resources, infrastructure and systems − it is industry that develops the medicines, treatments and technologies that have such a big impact on patients’ lives.

The first Discovery Forum meeting, held on 21st November 2017

Clearly, effective industry partnership also has the potential to deliver a boost to the UK’s economic health. The Government’s Industrial Strategy White Paper focuses on the Life Sciences as a growth driver − already bringing £64 billion a year to the UK economy and employing over 220,000 highly skilled scientific staff. Seizing the opportunities of the genomics sector will generate ever-stronger growth.

A catalyst for discovery

Building on learning from earlier industry partnership projects, Genomics England’s Discovery Forum marks an acceleration in our work to consolidate the UK as the global centre of genomic research, discovery and investment.

Fundamentally, the Forum aims to catalyse the entire genomics ecosystem: from small and specialised start-ups all the way through to the big pharma companies. The goal is to align the right companies with the right opportunities. It is a virtuous circle: high levels of investment stimulate the growth of new and existing businesses − which attracts the world’s best research talent − who create the most innovative technologies − which attracts high levels of investment.

Joanne Hackett

We held our first Discovery Forum in November 2017 and the appetite from industry was clear − with more than 120 attendees representing more than 50 companies from the genomics domain. Importantly, and for the first time, investors joined the partnership.

Content focused specifically on areas that industry has identified as important: effective engagement with Genomics England; access to information and research; and maximising the usefulness of the Forum network. Sessions included:

  • Progress of the 100,000 Genomes Project;
  • Genomics England’s commercial and IP strategy;
  • Genomics England’s data and research platforms;
  • The NHS genomics environment – presented by Professor Sue Hill, NHS England’s Chief Scientific Officer;
  • Understanding how to access research and the work of the Genomics England Clinical Interpretation Partnerships (GeCIPs)
  • Exemplars of work between industry and Genomics England.

Forum members were also able to ask ‘live’ questions during the event – using an interactive platform. Answers were either given in real time, or collected for later and more detailed responses.

Evaluation is a core objective of every Forum – ensuring that we continually deliver to industry need. I’m delighted to say that feedback from this meeting suggests we hit the ground running. We will carry this forward to our next Forum in March, as well as other global partnership opportunities such as our presentation on leveraging the UK lead in genomics in San Francisco on 8 January 2018.

Partnership − on an industrial scale

Genomics is made up of many moving parts − from the understanding and consent of the public, to truly pioneering research, to building an effective NHS infrastructure. But make no mistake, the Discovery Forum and the industry partnerships it builds are every bit as important to the success of genomic medicine.

As I said at the start of this blog, the time for talking about genomic potential is past. The time to talk to business − and forge partnership on an industrial scale – is now.

This post will also feature on the Digital Health London website:

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Genomics England Responds to Government’s UK Industrial Strategy

In response to today’s policy paper, “Industrial Strategy: building a Britain fit for the future” from the UK government, Sir John Chisholm, Executive Chair of Genomics England said:

“We welcome the Government’s Industrial Strategy. This will enable us to build on the UK’s global lead in population genomics, to drive NHS transformation, improve health outcomes and realise future economic benefits for the UK.

Genomics England is committed to building a world-leading UK genomics sector to deliver increasing patient benefit and to drive innovation, discovery and investment in our genomics industry.”

View our Industry Partnerships pages

Genomics England welcomes the appointment of new UK government chief scientific adviser

The Cabinet Office has announced this week the appointment of Dr Patrick Vallance as the new government Chief Scientific Adviser. Dr Vallance, who is currently President of Research and Development at GlaxoSmithKline, will take up the post in Spring 2018.

Sir John Chisholm, Executive Chair at Genomics England welcomes the appointment:

I am delighted at Patrick Vallance’s appointment as the new Government Chief Scientific Adviser. Patrick is one of science and technology’s strongest and most passionate advocates – built on deep experience of academia and industry. Patrick understands what the sector can do for the UK and I know that he will make a real and positive contribution working at the heart of government.


Official statement (opens in new tab)

PanelApp Version 2 Launched

A new and improved release of PanelApp

Visit our dedicated PanelApp page to learn more about our publicly accessible crowdsourcing tool for virtual human disease gene panel creation, storage and querying.

The diagnostic grade ‘Green’ genes and their modes of inheritance in the PanelApp virtual gene panels are used to direct the variant tiering process for the interpretation of genomes in the 100,000 Genomes Project.

What’s new in V2?

Direct URL links to panels or genes are available, even if you are not logged in

Straightforward links to genes e.g.

Shorter panel codes e.g.

  • Both Genome build GRCh38 and GRCh37 are supported
This includes updates to some HGNC-approved gene symbols.

New webservice queries are available; you can specify assembly GET parameters with either GRch37 (default) or GRch38 as a value.

Ensembl Ids will be returned for the specified assembly version: GRch37 version 82 or GRch38 version 90 if they exists in the database.

For example …/WebServices/search_genes/AKT2/?panel_name=Regional 20overgrowth 20disorders&assembly=GRch38

  • Improved page loading and greatly improved response times
  • Improvements to the registration process

Updated documentation will be available through PanelApp soon.

More PanelApp Updates

Summary of updates to Version 1 panels in October 2017

PanelApp October updates

PanelApp Update

  • 167 diagnostic-grade (Version 1+) panels
  • >540 registered users
  • >11,400 V1+ genes

Tissue Handling in the Royal College of Pathologists Bulletin

A recent article in the Royal College of Pathologists‘ bulletin provides a summary of our recent Tissue Handling Workshop.

Download PDF

One of the major challenges of the 100,000 Genomes Project has been collecting tissue samples from participants so that DNA can be extracted and sequenced.

Early experiments showed that how the samples are collected, stored and processed can affect the quality of the DNA, and therefore the success of whole genome sequencing, so a new objective emerged: to transform pathology services’ tissue handling practices in the NHS.

How could we better preserve and process tissue samples to make sure DNA remained as intact as possible, giving the highest quality genome sequencing further down the “pipeline”? We know that fresh tissue produces excellent Whole Genome Sequencing results. But, some pathologists hesitate to use refrigeration for fresh tissue sampling in case it affects other diagnostic tests.

However, as set out in this paper by our pathology experts, Professor Louise Jones and Dr Clare Craig, these same changes are seen in samples that are treated in the conventional way, i.e. placed unopened into formalin until they can be batched for sampling.

This is why diagnostic biopsies are used, where possible, in preference to surgical resection samples when immunohistochemistry or other testing that may have a clinical impact is necessary. Dr Craig said:

Thought should be given into the quality of the conventional approach before critiquing the quality of any new approach. Pathologists have a challenge ahead to navigate how best to handle tissues to enable optimal results with respect to morphology, immunohistochemistry and molecular pathology.

In addition to the article, we have sets of videos (available both here on the website and via Vimeo) covering:

  The Tissue Handling Workshop talks
  How to sample different tissue types – for pathologists

These videos have been accredited by the Royal College for Continuing Professional Development (CPD) credits; follow the links to request certificates.

We are also working on a short animation to describe how formalin damages DNA in tissue samples – watch this space for updates.

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