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Personal health data clouds to give early warning for cancer, other diseases

Around 228 000 people had their genomes sequenced in 2014, representing around 66 petabytes of data, or around a million Blu-ray disks. Image courtesy of ELIXIR
Around 228 000 people had their genomes sequenced in 2014, representing around 66 petabytes of data, or around a million Blu-ray disks. Image courtesy of ELIXIR

The falling cost of gene sequencing and the prevalence of healthcare monitoring gadgets means our bodies will become data clouds that give us an early warning for diseases like cancer and neurodegenerative conditions such as Alzheimer’s, according to researchers in a growing field known as computational medicine.

Data is everywhere, it affects the things we buy, the way we vote and the news we read. But in healthcare, it is changing how we approach wellness and diseases, allowing us to work out what illnesses we’re at risk of getting, and giving us the chance to take action before they strike.

‘Genomics is moving from the research lab into the healthcare system,’ said Niklas Blomberg, the director of ELIXIR, an ambitious project supported by the EU to create a Europe-wide infrastructure to give researchers access to biological data and research. ‘DNA sequencing allows doctors to predict the likelihood of their patient inheriting a mutation of these genes, and suggest preventive treatments.

The explosion of biological data has been driven by a meteoric fall in the cost of getting your DNA sequenced. It took thousands of people ten years to sequence the first human genome, whereas now it can be done in a few hours for less than EUR 1 000.

The issue is particularly relevant to Dr Jim Dowling, a senior researcher at the EU-funded BiobankCloud project, as both he and his wife are carriers of the mutation for cystic fibrosis, meaning that each of his children had a one-in-four chance of getting the disease.

If genetic sequencing had been widely available at the time, they would have been able to take measures to reduce the risk. In fact, both of his children have gone on to develop the disease. ‘That’s the kind of thing you could prevent with IVF (in vitro fertilisation),’ he said.

Traffic light dating

He believes that in 10 years genetic information will become so widespread that people will access their genetic data using their smartphone. It could be used, for example, to tell potential partners if their children would be at risk of disease.

‘The cliché is a traffic light dating system,’ he said. ‘Before you talk to someone you’d check, what does the traffic light say.’

‘What we see in terms of the not very far future is that the body will be a digital object.’

Dr Jesper Tegnér, Karolinska Institutet, Sweden

Already around 228 000 people had their genomes sequenced in 2014, according to Illumina, a US-based gene sequencing company, which including backups could represent around 66 petabytes of data, or around a million Blu-ray disks.

Dr Dowling explained that the BiobankCloud project has been developing a way to store and read this data quickly, using the same technique that services such as Google use during a search query, and it plans to release the software this spring.

It works by dividing the data between hundreds of machines and then analysing all of them at the same moment.

‘If you read my genome from a single disk it’ll take a thousand seconds, but what big data is about is taking my genome and splitting it up over a thousand machines,’ he said. ‘When you send a computation you send it to all thousand machines.’

Monitored self

These developments come as people also collect health data using gadgets such as the Fitbit monitoring wristband, while smartphones record how far we walk and where we go, giving researchers a more complete view of what happens to our bodies when we are healthy and when we get sick.

‘What we see in terms of the not very far future is that the body will be a digital object,’ said Dr Jesper Tegnér, director and strategic professor of computational medicine at the Karolinska Institutet in Sweden. ‘Every individual will be a data cloud.’

Researchers like him have coined the phrase ‘systems medicine’ to describe the way that all of these kinds of data can be combined to give doctors a better understanding of how diseases affect different systems in the human body.

As well as DNA, systems medicine includes other types of data such as the actions of gene messenger molecules known as RNA, proteins, and information on how our genes react to the environment.

‘You need to look at not just a static blueprint in terms of DNA but you need to look at how it is used in different cells,’ he said. ‘What we see is the convergence of a rich amount of molecular data of different kinds, and interestingly, sensor data from smart devices which together defines your degree of wellness and propensity for disease.’

Dr Tegnér is a leading researcher on the EU-funded CASyM project, which is looking at how this explosion of data will affect the future of medicine. The project has produced a roadmap document to outline what’s needed to implement systems medicine in Europe.

‘The early adopters are already trying this, but on a mass scale (it will be available) maybe in 10 years’ time, not more than that,’ he said.

It could be used, for example, to tap the body’s immune system for an early warning when we are developing cancer or to help lessen the risk of Alzheimer’s disease.

‘The immune system generally attacks and tries to prevent us from having tumours, attacks the different cancer cells, so you will see changes in the immune cell early on when you have some kind of illness so that’s an interesting area within cancer,’ he said.

Open data

Researchers say the biggest hurdle for the use of big data in medicine is in the regulations, because if access to gene data ends up being controlled in the same way that medical records are in many countries, the data won’t be able to be passed on for research purposes.

It’s now, in the early stages of big data medicine, that the legal groundwork has to be laid to open up access to people’s medical data to researchers who can use it to look across the population and identify which signs can give us an early warning of disease.

‘The European Commission could have an important role to play here so really pushing for this open system where individuals have the right to their own data,’ said Dr Tegnér. ‘We see this as a very important issue.’

ELIXIR

ELIXIR is an inter-governmental organisation that helps Europe’s life science organisations manage and safeguard public research data, which is generated every day in massive quantities.

It is designed to help life science researchers capitalise on this ever-expanding store of biological data and facilitates research in areas such as medicine, biotechnology, food, agriculture and biodiversity.

ELIXIR consists of a central hub in Cambridge, UK, and a number of centres of excellence across Europe. It has been selected for EU support by the European Strategy Forum for Research Infrastructures.

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