Month: June 2017

The National Initiatives Meeting – genomics around the globe

Three years after the launch of the Global Alliance for Genomics and Health (GA4GH) and six months after the first GA4GH-hosted convention of national genomics initiatives, Kathryn North (Australian Genomics) and Genomics England’s Chief Scientist, Professor Mark Caulfield recently convened representatives from 13 National Initiatives in genomic data collection to discuss areas of potential collaboration at the Wellcome Trust in London.

Genomics England logo

The goal of the meeting was to identify potential areas of collaboration, resource and expertise sharing, as well as common needs across National Initiatives that GA4GH can incorporate into its “toolbox” of data sharing standards and tools.

The meeting was attended by representatives of major population-sequencing endeavours, from: Australia, Brazil, Canada, Finland, GenomeAsia100k, Global Gene Corp (India), the Netherlands, Qatar, South Africa, Switzerland, Turkey, the USA and the UK.

The three more established projects – Genomics England, Australia and the USA gave detailed talks about progress to date and challenges they have faced. This was followed by presentations from all of the emerging projects – covering their aims, funding models, disease focus, and resources they’ve developed. There were also workshops on Data & Sharing, Regulation, and Clinical & Education, as well as a round-table discussion.

Sir John Chisholm​, Executive Chair of the Genomics England Board, spoke on his vision for genomic research:

We are all engaged in the most significant program of the human race in the 21st century. If we’re successful, we’ll change the human experience from what it had been throughout history and evolution—that health is something which gets done to you by some force outside of you—to something you have control over.

This change is possible because we will soon be able to understand the genome, and to use it to predict outcomes.

“It’s a fantastic vision, but it’s very hard and it will take most of rest of the century to get there,” said Chisholm. He cited two challenges in particular:

1. Genomic medicine involves “colossal” amounts—millions, tens of millions, or even 100s of millions—of data points. This scale is necessary because of the low probability of making connections between the genome and human health.

Additionally, because very few associations are monogenic, combinatorial problems make unpacking the genome a very difficult and complex pursuit. In the past, scientific programs have built individual research cohorts for each study. This will not work with clinical genomic research, because no organization has enough money to fund research cohorts at this scale.

The only way to achieve cohorts of the size needed is by aligning fully consented patient data from the healthcare system with genomic data. No one country will be able to do this alone so national programs must collaborate.

Given that no one country can do it alone, nations must agree on rigorous standards and protocols, as artefacts of non-harmonized data collection processes will make it impossible to understand outcomes across a combined data set.

2. Implementing standards and protocols in routine healthcare will be difficult, Chisholm said, “but it’s something where the prize is so great, it’s worth doing.” In the four years since it was launched, Genomics England has spent considerable effort and made progress on the development of standards and protocols for data collection and getting them implemented across the UK’s National Health Service.

Now, he said, that needs to be taken to the international stage. He invited meeting attendees to “form a club” to work together to agree on standards and protocols for clinical genomic data sharing. This will allow for federated data sharing that is protective of participant confidentiality and privacy and enables “this transformation of the human experience in the 21st century.


In closing remarks, Professor Mark Caulfield said that the groups present must showcase their achievements to patients and the public in order to promote further involvement from those communities. Doing so, he said will result in “more ‘Denmarks’ and less places where we lock data away.”

He also summarised a number of high level themes emerging from the meeting:

  • In three years, the discussion has moved from a focus on future goals to examples of established infrastructure and large-scale genomic data collection in health care systems around the world
  • The next step is to position healthcare against research in order to achieve the needed scale, and to move from cohorts of 1 million individuals to 5 or 10 million thanks to shared data across the globe
  • This will require an ethical framework and robust guidelines for follow up
  • Initiatives must engage with patient advocacy and support groups since those populations are willing to take on challenges that researchers shirk from
  • Industry is vital to this endeavor, as it requires millions (or billions) of dollars
  • There is a need for robust IP that allows for freedom to operate, and the ability to account for situations where the responsible act is not to protect IP but to give it away

Project Milestones for our Genomic Medicine Centres

This month we’ve been celebrating four milestones for our brilliant recruitment teams across the country. The 100,000 Genomes Project could not exist without all the hard work of multi-disciplinary teams on the front line in the clinic, who speak to patients about the project and sign them up to be involved as participants.

NHS England established the Genomic Medicine Centres (GMCs) and clinicians based in those areas are working hard to find more people eligible to join the project.

Congratulations to the following GMCs that recently achieved these incredible numbers!

Christine Mather, aged 72, former Medical Director’s PA from Sale, was asked to take part in the project as she was suffering from polycystic kidney disease (also known as ADPKD). She was happy to give a blood sample as she understood that it may help others with the same condition especially as it is known to be inherited. She said:

I don’t want my daughter to have to go through the problems that I have. As soon as they find a cure it will be very good for future generations of my family as well as everybody who has it.

Christine is a patient at Dr Grahame Wood’s specialist ADPKD clinic at Salford Royal, and he said that recent trials have given great hope that new treatments for ADPKD can slow or even reverse this usually progressive disease.

Toby Williamson was born after a normal pregnancy, but it soon became apparent that he was not feeding well, was sleepy and passive and had poor eye control. Tests established that he had abnormally low muscle tone with global developmental delay leading to a visual impairment and severe learning difficulties which means his communication skills are very limited and all non-verbal. His mum, Charlotte, said:

He has the learning age of about a nine-month-old and the physical ability of just over a one-year-old. He relies on us totally for all of his personal care and all of his needs have to be met you have to constantly listen out for him, be aware of things for him.

Toby’s subsequent medical history has included regular ear infections and burst ear drums (upsetting his hearing, balance and learning); reflux, leading to hospitalisation for dehydration and subsequent medication; a squint, corrected by surgery in 2004; a diagnosis of Autism Spectrum Disorder in 2010; and many genetic tests – none of which have yet found a cause for his condition.

For years Holly and her husband were told that Antony, now aged 8 was born with global development delay, and suffered from challenging behaviour that he would grow out of. Three years ago the family were told he suffers with autism, but although the findings were a “relief” there’s still more the family want to know. Holly, who now cares for him full time, said:

Any results could make a big difference to his future, and even if there’s some result, no matter how big or small, it would be great news for us.

The Wessex NHS GMC serves 3.5 million people from Dorset, Wiltshire, Hampshire, Isle of Wight and parts of Somerset, Surrey and Sussex. Every sample collected can ultimately contribute to a report that will go back to a participant and their family, and the wider research effort that will use the huge datasets generated from sequencing samples’ genomes.

Thank you for all your hard work, and to all our participants who’ve signed up so far!


Resources:

  • Consent – for healthcare professionals and participants
  • Results – what can participants find out?
  • Research – joining the research community in the Genomics England Clinical Interpretation Partnership (GeCIP)