David Atkins was invited to present on the UK approach to bring genome sequencing to clinical practice at the third meeting of the Program Personalised Medicine, a collaboration of ZonMw, KWF Cancer research and Zilveren Kruis.

The NHS, UK’s national healthcare provider, focuses on rare diseases to accelerate and improve diagnoses and to improve therapeutic support. The motivation for this initiative is an awareness that the current gold standard for diagnosing rare disease patients is a time consuming and expensive process. Furthermore, initial studies suggest that a significant portion of patients receive either the wrong or inadequate therapy.

The 100,000 Genomes Project (2014-2018) was initiated in 2012 by former Prime Minister David Cameron and led by Genomics England, a Company fully owned by the Department of Health in partnership with the NHS. The 100,000 Genomes Project aimed to benefit patients by ultimately providing appropriate diagnosis and increase the chances of effective therapy, to enable biomedical research, to stimulate the genomics industry in general and to promote ethics and transparency.

In 2018 Genomics England chose Congenica as its Clinical Decision Support Service partner for the delivery of clinical genomics to NHS England. Congenica’s selection was based on their software platform called Sapientia. Sapientia was developed over several years with a number of collaborators including the clinical research centres participating in the early stages of the 100K pilot.  The reasons for selection of Sapientia as the preferred clinical interpretation platform was due to the higher diagnostic yield achieved (43% for all cases assessed by Sapientia) and the ability to manage, move and store WGS samples at significant scale. Congenica has also developed customer support capability that includes training, trouble shooting and a customer support hotline. In 2019 Congenica rolls out the clinical implementation of the sequencing reporting system for all British clinics of the NHS.

Why it is so important to address rare diseases by using genomic data

‘Rare disease’ is a terrible name for such a common problem, Atkins explained whilst lining out the numbers:

Needless to say, that wrong and/or late diagnoses and inappropriate therapy on a large scale are very expensive, moreover they create an diagnostic odyssey in which patients and their families are bounced around.

Champions and sponsors are key. “For the take-off of the 100,000 Genome Project it was David Cameron, but they may also be patients, their families, other partners. Find the people who will defile logic and have belief and passion.”

Making the use of genomic data accessible, routine and ubiquitous: the challenges

That said, making the use of genomic data accessible, routine and ubiquitous comes with a number of challenges:

  1. The biggest barrier in delivering genomic medicine to the clinic has always been its expense. According to Atkins this problem has now been largely solved: genome sequencing is nowadays much more cost-effective than it used to be.  
  2. Data handling on analysis is massively underestimated. The focus is mostly on sequencing, whereas processing the data is also of huge importance.
  3. Another large problem is the issue of health economics, something that every new medical technology has been going through in the history of healthcare. We see penetration only going so far as a private or public payer joins. In most parts of the world the discussion about the payment is happening at this moment.
  4. Regulatory approval: how do we see ourselves being regulated? Many countries haven’t thought about this challenge, Atkins points out. The new In-Vitro Diagnostics Regulation will cover this aspect.
  5. The massive challenge of workforce development and education. The amount of genomic data that’s coming our way in the next two years can probably be captured by only two percent of the counsellors. It’s of huge importance to address this problem and to keep counsellors educated. Developing automated counselling for simple purposes could be part of the solution to yield the shortage of counsellors.
  6. Involve and educate patients. Any national program needs a large number of patients. In the United Kingdom the patient engagement is very high and is therefore a good example for other countries. Individuals should be motivated and mobilised to cooperate.

Growth of Clinical Genomics in the UK

The vision of the original Genomics England 100,000 genomes project was considered ambitious when it was first communicated several years ago. The goals were expanded significantly in October 2018 with the announcement by the Secretary of State for Health and Social Care of the goal to sequence 5 million genomes “within the next 5 years”. By all accounts the final details are to be finalised as it relates to the source of the genomes and funding, but the scale of the ambition has been inspirational to all those involved in clinical genomics in the UK. Without question this will continue to support the aims that lead to the development of the original pilot project of 100K genomes.

What is the benefit of the European 1+Million Genomes project, in which the Netherlands participates, when the UK will have 5 million genomes, Atkins is asked during his presentation?

The benefits would be like those anticipated by the investment in Genomics England that begins with and Improvement in the clinical genomics infrastructure, formation of a valuable Dutch genomics resource, new skills and capabilities and potentially an emerging industry. These in turn will elevate the standard of clinical care that will both help Dutch citizens and potentially reduce the cost burden.

Lessons learned so far

Atkins ends his talk by sharing the lessons he has learned during his journey from genomic data to personalised health care so far.

  • Partnership and planning are key.
  • Expect delays and build contingency. “In any software development program you get roughly a third of what you had planned, it’s the same in genomics. We have now over 40 engineers, but we really want to scale up to address this problem.”
  • Allocate sufficient resources.
  • Involve all stakeholders at every stage. “Commercial partners, the NHS, but also participants and their families. Anything you do, do it public.”
  • Develop test data as early as possible. “Genomics has anything to do with software”
  • Training and retraining is essential. “It’s one of these things that’s so unlike other procedures. There’s so much change in a database, it’s not static. So bear in mind that the training budget is always involved in your planning.”

> Read the full report of the meeting



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