Genomics England selects QIAGEN hereditary and rare disease solution

Genomics England today announce that it has selected QIAGEN’s HGMD® Human Gene Mutation Database for the 100,000 Genomes Project. HGMD is the leading content knowledgebase for interpretation of genomic data in hereditary and rare diseases, providing a deep resource of expertly curated data from the world’s scientific and clinical literature.

The 100,000 Genomes Project will use QIAGEN’s HGMD Online Professional solution, which is part of the QIAGEN Clinical Insight (QCI) portfolio of solutions for the interpretation of complex genomic data, to support scientists, clinicians and researchers in 13 NHS Genomic Medicine Centres for clinical reporting and interpretation.

“Rare and hereditary diseases can lock patients, families and healthcare providers in a long, difficult diagnostic odyssey, and 100,000 Genomes is a cutting-edge NHS program to gather and analyze whole genomes from a large cohort of patients in search of causes and future treatments,” said Dr. Laura Furmanski, Senior Vice President and Head of QIAGEN’s Bioinformatics Business Area. “We are honored to deepen our collaboration with Genomics England. QIAGEN’s industry-leading bioinformatics solutions, including cloud-based HGMD content, will help 100,000 Genomes derive actionable insights from a massive pool of next-generation sequencing data. We are pleased to be selected.”

“We are delighted to work with QIAGEN’s bioinformatics solutions as a comprehensive resource for manually-curated analysis and interpretation content. High-quality interpretation of genomic data in the 100,000 Genomes Project will provide deeper insights into rare inherited diseases, and ultimately lead to more diagnoses and tailored treatments for patients”, said Dr. Augusto Rendon, Director of Bioinformatics for Genomics England.

QIAGEN Bioinformatics offers a portfolio of industry-leading solutions for the analysis, interpretation and reporting of biological data. Products include Ingenuity, CLC bio and OmicSoft software and databases. As part of the QIAGEN Knowledge Base, HGMD is the gold standard for expertly curated content from peer-reviewed publications on human inherited disease mutations. HGMD has been cited in more than 5,000 scientific publications. For more information, please visit

Intellia Therapeutics joins the GENE Consortium


Today (12 January 2017), Intellia Therapeutics has joined the Genomics England Genomics Expert Network for Enterprises (GENE) Consortium, as the first dedicated genome editing company to participate in the 100,000 Genomes Project.

The GENE Consortium, established in March 2015, is the 100,000 Genomes Project’s industry partnership.  Intellia will join 12 other companies who are working together in a pre-competitive trial. The collaboration aims to identify the most effective and secure way of bringing industry expertise into the 100,000 Genomes Project to realise future potential benefits for patients affected by rare diseases or cancers.  Members of the consortium are granted controlled access to aggregated, de-identified genome and health data of participants.  They work alongside experts that specialise in data analysis, so that the project can benefit from cutting edge advances in handling Big Data.

Genomics can greatly improve our understanding of health and disease, unlocking new treatments or repurposing existing treatments based an individual’s genomic makeup; so-called personlised medicine.

Sir John Chisholm, Executive Chairman, Genomics England, said: “The potential for genomics to transform healthcare, from better diagnoses to new drugs and treatments, is extraordinary.  We are delighted to welcome Intellia Therapeutics to our GENE Consortium.  The UK is a global leader in population sequencing and it’s important for the future of medicine that we continue to attract and collaborate with the most innovative emerging technologies in this space.”

“Access to genomics information is critical as Intellia looks to better understand the basis of disease and to develop potential genome-editing treatments,” said Intellia’s Chief Executive Officer and Founder, Nessan Bermingham, Ph.D., “We look forward to actively participating in the GENE Consortium, as Genomics England is enabling scientific exploration and key medical insights that ultimately will benefit patients.”

A Year of Conversations about Genomics

By Vivienne Parry OBE, Head of Engagement at Genomics England

When we began the 100,000 Genomes Project, our initial engagement work was with potential participants, affected both by rare disease and cancer. We wanted to know what their principal concerns were. They turned out to be both practical – for instance, what the impact of results might be on their families or if they might be disadvantaged financially by taking part – and ethical, such as use and access to their data. We made sure that we addressed these issues in our subsequent patient literature and other support material. We continue to work with participants through our Participant Panel. They are involved in many different aspects of the Project’s work. For instance, project participants sit on the group that considers applications to access the 100,000 Genomes dataset.

Identifying the key issues

For most patients, the use of genomics in medicine has clear benefits; for diagnosis, greater understanding of their condition and for the development of new treatments, not for them but for others like them in the future. Their views about the issues raised by genomics are coloured by their own experience and are different to those of the general public. But for genomics to be transformational, we need the wider public to be comfortable that the issues raised have been debated and where necessary, addressed. We also needed to know where to focus our engagement efforts in the future.

Working with a variety of partners

We began a year long ‘conversation’ with a variety of public audiences across England; young, older, those likely to have some knowledge, those with none, professionals and politicians, working with a variety of partners including the British Science Association, the Science Museum, University of the Third Age and Verge Magazine.

Socialising the Genome

Drawing from the #glitch animationBut before we began, we wanted to find out how people talked about the issues raised by genomics and what words and language would help them. Social scientist and genetic counsellor Dr Anna Middleton carried out a series of focus groups discovering that people knew more than they thought they did, even if they couldn’t explain it in correct technical terms. Her findings were translated into a series of six films, developed by advertising guru Julian Borra. Online audiences were then able to comment in order to find out what terms and language resonated best with wider audiences. You can find the films here and tell us what you think.

The results of the Genomics Conversation are fascinating and there is a full report here which I urge you to read. There is plenty of nuance as you would expect but there are also some universal red lines. One example is that insurers and marketing companies should not be allowed to access an individual’s genomic data.

We have outlined our next steps:

  • We need to bridge the gap between how professionals speak about genomics and how the public talk about it
  • We need to begin a major programme of work with cancer patients and with older people (the group most likely to be diagnosed with cancer) to find out if their views are different to those of rare disease patients and how best to tailor communications material for them
  • Concerns about commercial access to data were mentioned frequently and we will be working with a number of partners including the new independent taskforce ‘Understanding Patient Data‘, set up by the Wellcome Trust
  • Commercial access to the 100,000 Genomes Project data is critically important if new medicines and treatments for patients are to be developed. We need to work with industry and with other partners to build trust, showing how industry develops medicines and diagnostics.

We are entering a new era of medicine. We must make sure that we both understand and address the concerns of the public and that we earn and continue to retain their trust in this transformational medical advance.

Download the full report here.

Findings from the National Consent Evaluation

By Dr Caroline Benjamin, National Service Evaluation Project Lead and Guild Senior Research Fellow, University of Central Lancashire

Earlier this year, I and colleagues from NHS Genomic Medicine Centres were asked to deliver an evaluation with the aim to further improve the quality of the consent process and materials in the 100,000 Genomes Project.

On behalf of the project team leads, Markella Boudioni (Imperial College London), Eliot Marsden and Antje Lindenmeyer (University of Birmingham), I am pleased to present the results from ‘The National Service Evaluation of the Consent Process and Participant Materials used in the 100,000 Genomes Project’. This evaluation has been a collaborative effort, led by the North West Coast Genomic Medicine Centre,  between the Genomic Medicine Centres, Universities, NHS England and Genomics England. We would like to thank the 100,000 Genomes Project participants, recruiters and focus group members who provided feedback.

The Report will assist Genomic England’s current review of the consent documentation and process, and you can download the full report and summary here. A Background Document is available directly by contacting a member of the project team.

We  encourage wide dissemination of the findings and encourage debate and ongoing evaluation of the consent process for whole genome sequencing within clinical care and transformational projects.

Photo of project team

Project team. L-R: Caroline Benjamin, Markella Boudioni, Antje Lindenmeyer and Eliot Marsden.

UK Prime Minister Opens New Sequencing Centre

Today (21st November) Genomics England, Illumina, and the Wellcome Trust Sanger Institute hosted the UK Prime Minister, Theresa May, at the opening of the Bridget Ogilvie Building on the Wellcome Genome Campus in Cambridge. This is where DNA sequencing for the 100,000 Genomes Project takes place.

Mike Stratton & Theresa May. Credit - Sanger Institute, Genome Research Limited.

Mike Stratton & Theresa May. Photo Credit – Sanger Institute, Genome Research Limited.

It is also the site where the UK’s contribution to the original Human Genome Project took place over 15 years ago. The campus is now home to some of the world’s foremost institutes and organisations in genomics. There is now have a real opportunity to turn discoveries about genomics into healthcare benefits for NHS patients. The 100,000 Genomes Project is currently the largest whole genome sequencing initiative of its kind in the world. It aims to harness the potential of whole genome sequencing within routine NHS care.

People currently taking part in the Project are NHS patients with rare diseases and their families, as well as patients with certain common cancers. Those who take part are set to benefit through better diagnoses and personalised treatments.

Researcher working at an illumina X10 sequencing machine, Oliglive Bulding, Wellcome Genome Campus, Cambridge.

Scientist working at an Illumina sequencing machine, Ogilvie bulding, Wellcome Genome Campus, Cambridge.

Almost 15,000 whole genomes have now been sequenced in the 100,000 Genomes Project. There are 13 NHS Genomic Medicine Centres across England who are continuing to recruit patients. Biotech company Illumina are undertaking the genome sequencing. Genomics England, together with clinical interpretation partners are interpreting those sequences to return results to patients and clinicians.

As part of the opening, Sir John Chisholm, Executive Chair of Genomics England was introduced to the Prime Minster along with Dr Dame Bridget Margaret Ogilvie and David Bentley, Vice President and Chief Scientist of Illumina. They then showed her the work going on in the sequencing centre along with Chief Scientist at Genomics England Professor Mark Caulfield and Chief Scientific Officer for NHS England, Professor Sue Hill.

Sir John Chisholm, Executive Chairman of Genomics England said;

The UK is recognised across the world for being the first nation to introduce whole genome sequencing at scale in routine care environments. The Ogilvie facility is central to that achievement and opens the way to the virtuous circle of treating patients with genomic medicine leading to knowledge creation leading to advanced therapies leading to superior health outcomes.

Professor Mark Caulfield, Chief Scientist for Genomics England said;

NHS patients will be the first to benefit from discoveries made from this project.  The 100,000 Genomes Project Genome Sequencing Centre has already enabled us to feedback results to participants with rare diseases who had not achieved a diagnosis through routine healthcare

UK Prime Minister Rt Hon Theresa May, said;

It is an honour to open these buildings as they truly represent cutting edge British science and business in the modern era. What I’ve seen on the Wellcome Genome Campus is an excellent example of research from across the UK and around the world coming together with commerce to deliver benefits for everybody including patients in the NHS. We want the UK to be the ‘go to’ place for scientists, innovators, businesses and investors. This really is a very good example of that.

Professor Sue Hill, Chief Scientific Officer for NHS England said;

This collaborative partnership working with the latest sequencing and interpretation technologies will provide improved  diagnosis and treatment options for patients; and support research and further learning into how we understand and treat disease.

NHS England is proud to support clinicians in our 13 NHS Genomic Medicine Centres in harnessing this technology for the benefits of their patients, particularly those who suffer from cancer and rare diseases.  The 100,000 Genomes Project is putting the NHS at the forefront of genomic medicine internationally, and will form a platform for the wider uptake of personalised medicine approaches in years to come.

Professor Sir Mike Stratton, director of the Wellcome Trust Sanger Institute and chief executive of the Wellcome Genome Campus, said:

Genomes and biodata are an important part of all our futures. The Campus is home to research institutes, spin-out and start-up companies, academic-industry partnerships and Genomics England; all dedicated to driving and leading pioneering research and innovation and discourse in the sphere of genomes and biodata.

The new buildings mark the next major step in the progression of our vision for this Campus as a global hub for genomics and biodata. We have an ambition to translate and commercialise research findings, as well as inform and enable the NHS to integrate genomics into clinical care.

David Bentley, DPhil FMedSci, Vice President and Chief Scientist, Illumina Inc. said;

It was an enormous pleasure to host the Prime Minister, Rt Hon Theresa May MP, and demonstrate the importance of industrial partnership for patient outcomes and sustained change.

With the building of our new headquarters for Europe, Middle East, and Africa at Granta Park, Cambridge, Illumina’s inward investment to the UK is set to continue along with our projects to support the NHS, and we have every confidence in the country’s unique position to be a leader in genomics in the forthcoming revolution in personalised medicine.

More information

About the 100,000 Genomes Project

About the 100,000 Genomes Project

Video introduction to the 100,000 Genomes Project.

diagram of DNA mapping

Understanding Genomics

Find out about DNA, sequencing and genomics.

Genomics plc Appointed as Analysis Partner for the GENE Consortium


Genomics plc, a leading analysis company developing an integrated platform to uncover the relationships between genetic variation and human disease, today announced that it has been appointed as Analysis Partner for the Genomics England Genomics Expert Network for Enterprises (GENE) Consortium. Genomics plc will be analysing genomes at an unprecedented scale and, together with the company’s existing knowledge base, be providing insights into human biology that will help to inform pharmaceutical R&D investment decisions.

Genomics England is delivering the UK 100,000 Genomes Project – whole genome sequencing rare disease and cancer patients in the National Health Service. Genomic information has huge potential to transform drug development pipelines, and one of Genomics England’s four main goals is ‘to enable new scientific discovery and medical insights’. To that end, in 2015, it set up the GENE consortium, which included major pharmaceutical companies such as Abbvie, AstraZeneca, Biogen, GSK, Roche, Takeda and UCB. With a focus on patients with rare diseases and cancers, over 13,000 genomes have already been sequenced and, within its secure IT infrastructure, de-identified data are being made available to Consortium participants to accelerate the development of new diagnostics and treatments for patients.

The power of genomic data to gain novel biological insights grows with both the scale of the data and the breadth of associated physical and biological information. Genomics England’s genetic information is increasingly linked to electronic medical records, a rich source of such phenotypic data, but one that adds many dimensions to the complexity of the analysis challenge.

Understanding and using such datasets to their full potential requires an in-depth understanding of genomics, sophisticated statistical analysis approaches, creative visual representations, computationally efficient algorithmic design, a dedicated IT infrastructure, and an expert team of scientists and IT engineers. Since its formation in early 2014, Genomics plc has been building a powerful platform combining these elements along with a database of genetic and linked phenotypic data on almost 3 million individuals that seamlessly integrates results from over 700 genetic studies across over 500 phenotypes, the largest dataset of its kind in the world. It is also collaborating with major pharmaceutical companies including Biogen, Eisai, Merck and Vertex, as it applies its integrated platform across all areas of pharmaceutical R&D, including target validation, assessment of on-target safety effects and discovery of repositioning opportunities.

Financial terms were not disclosed.

John Colenutt, CEO, Genomics plc, said: “We are excited to be working with Genomics England on the world-leading 100,000 Genomes Project. The use of human genetic data is increasingly recognised as a mechanism to transform productivity within the pharmaceutical and diagnostic research and development industry, and we look forward to working with the GENE Consortium, its members, and others within the sector to improve human health and reduce healthcare’s economic burden.”

Sir John Chisholm, Executive Chair, Genomics England, said: “The potential for genomics to transform healthcare, from better diagnoses to new drugs and treatments, is extraordinary, and we are delighted to work with Genomics plc, a proven leader in the field of genomic analysis, to maximise the value of the 100,000 Genomes Project for patients”.

Visit the Genomics plc website here.

North Thames Genomic Medicine Centre celebrates Jeans for Genes Day by reaching 4000th participant

The North Thames Genomic Medicine Centre (GMC) has today announced that more than 4,000 people from the network have taken the opportunity to have their genome sequenced in the 100,000 Genomes Project. The North Thames GMC is one of 13 centres set up by the government to help researchers and scientists gain a better understanding of the genetic causes of rare diseases and cancer so that more effective treatments can be developed.

Professor Lyn Chitty, clinical lead for the NTGMC, said: “It is fantastic that so many people in our region have been able to take part in the project. By sequencing genomes, we have the ability to identify the cause of conditions that have previously been undiagnosed, helping understand these conditions better as well as offering the potential to develop more effective treatments.”

The programme is particularly powerful for people with undiagnosed rare diseases as it allows early diagnosis and helps conditions be managed more effectively. Earlier this year, the first children in the country received their diagnosis through the 100,000 Genomes Project at Great Ormond Street Hospital. As well as removing uncertainty for families, the results received through the project help people to consider future treatment options, social support and family planning.

The North Thames GMC will very soon see more results from genome sequencing being returned to clinicians and their patients. Watch this video to find out more about how the 100,000 Genomes Project can help people – Jessica’s Story. People who are eligible to take part in the project will be identified by their doctor and asked to if they would like to take part by providing samples for genetic sequencing.


About the North Thames NHS Genomic Medicine Centre

The North Thames GMC is a partnership between seven NHS trusts, led by Great Ormond Street Hospital. The partners are:

  • Barts Health NHS Trust
  • London North West Healthcare NHS Trust
  • Moorfields Eye Hospital NHS Foundation Trust
  • Royal Free London NHS Foundation Trust
  • Royal National Orthopaedic Hospital NHS Trust
  • University College London Hospitals NHS Foundation Trust (UCLH)

The centre primarily recruits patients from the north and east of London, Essex, Hertfordshire and Bedfordshire but, due to the wide geographical spread of rare diseases in the UK, it also collects samples from patients across the country who are referred for treatment at our hospitals.


GenomOncology’s Knowledge Management System to analyse cancer samples in the 100,0000 Genomes Project

GenomOncology logo

Genomics England is partnering with GenomOncology LLC (GO) to utilise the GO Knowledge Management System (GO KMS) as a tool for clinical reporting enablement.

Genomics England will integrate the GO KMS as a key content driver to augment clinical reporting in the 100,000 Genomes Project’s cancer programme,  coupling Genomics England curated database with the GO KMS’s data for a comprehensive clinical report comprised of the most relevant drugs, prognoses, and clinical trials.

The GO KMS enables Precision Medicine by allowing users the ability to aggregate and analyse biomarker-based data.  The GO KMS leverages a large number of existing data sources including FDA, NCCN, and ASCO guidelines as well as providing exclusive API access to the expertly curated data of My Cancer Genome®. The GO KMS allows users to analyse genomic variants within a ‘genomics-aware’ framework that includes a diverse set of annotations including genes, pathways, drugs, alterations, transcripts, and a disease ontology.  In addition, the GO KMS is designed to empower researchers and clinicians alike to build and maintain their own curated knowledge repositories.

GO and Genomics England will work through an initial implementation phase that will focus on extending the GO KMS to include NICE Guidelines and UK-specific clinical trials, as well as a variety of other enhancements to support clinical reporting, leading to more personalised care for NHS patients.

Augusto Rendon, Director of Bioinformatics at Genomics England said: “GenomOncology brings to the table a widely used knowledge base, as the people behind My Cancer Genome. Their data was easy to integrate into variant annotation and interpretation pipelines due to their consistent variant nomenclature. Through exhaustive curation GenomOncology has made great progress in solving the difficult problem of representing cancer variants consistently in order to support genomic workflows”.

Visit GenomOncology’s website here.

The Journey

Getting results in the 100,000 Genomes Project – The Journey

The first attempt to sequence a whole human genome took 13 years – all 3 billion letters of the genetic code. Super fast new technology means this can be done in as little as 24 hours today.

In practice, because we batch genomes together for efficiency, it takes us 3 days to sequence a whole genome.

But sequencing is only the beginning.

Looking for a needle in a haystack

When we look at your genome, we are looking for a needle – a glitch – in a vast haystack. The first thing we need to do is make the haystack a bit smaller.

Luckily human genomes are 99.8% the same. But that’s still around 4 million potential differences, most of which are healthy variations that make us the individuals we are.

Sequencing your genome produces two files of info. One is the raw data – all six billion letters. The other is what’s called a variant call file. That’s the 4 million. This is the ‘small’ haystack we now work with.

The process so far has largely been automatic. (Though at the time we started this project, no-one in the world had sequenced 100,000 whole genomes – and we’ve made something sound easy that even 5 years ago would have been thought impossible. Hats off to Illumina who do this for us in Cambridge.)

Next comes the bit that takes the time.

Call in the Bioinformaticians

Bioinformaticians – scientists who are brilliant at organising information and spotting patterns – trawl through the 4 million, looking for the glitches that might possibly account for someone’s symptoms. They decipher how each one might affect a person and pull from the many, many hundreds of potential ‘needles’ – changes that might possibly be responsible for a problem. This bit is called ‘annotation’.

But they’ve still got hundreds and hundreds of potential suspect glitches. A small haybale’s worth.

“Trawling through the 4 million used to take a year or more.”

Some of these now get discarded thanks to a filtering system which uses special tools that can access huge databases of knowledge. Out for instance go changes where there’s good evidence that they’re commonly found in the population and don’t cause a problem. Out also go changes that don’t fit the disease in your family.

National Training Consent Day

Join us in September to learn the skills and knowledge required to recruit and consent patients to the 100,000 Genomes Project.

HEE’s Genomics Education Programme in conjunction with the Birmingham Women’s Hospital Clinical Genetics unit and the West Midlands Genomic Medicine Centre (GMC) education team will be hosting a National Consent Training Day on Tuesday 20th September in central Birmingham.

The aim of the day is to introduce and demonstrate the use of a blended learning package that is designed to equip health professionals with the skills and knowledge required to recruit and consent patients to the 100,000 Genomes Project.

The package incorporates the Genomics Education Programme’s ‘Preparing for the consent conversation’ online training course and training materials that can be used in face-to-face sessions.

We would like to invite individuals from each Genomic Medicine Centre (approximately three from each centre) to attend this event. Ideally these representatives will be the individuals who will provide consent training within their GMC. Please email Charlotte Szczepanik if you would like more information or with the details of who will be attending. The location of the meeting will be confirmed in the coming weeks.

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