Month: November 2017

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:

Read more

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.