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Cancer genomes everywhere: lessons learned from the Festival of Genomics

28
Jan
2019

Cancer featured prominently as scientists from around the world met recently at the Festival of Genomics conference in London. Dr Keith Bradnam, the ICR’s Digital Strategy Manager, was in attendance to see talks by ICR researchers and find out about the latest developments in cancer genomics.

Posted on 28 January, 2019 by Dr Keith Bradnam

Professor Mark Caulfield giving keynote talk at Festival of Genomics 2019

Professor Mark Caulfield, Chief Scientist at Genomics England, giving the opening keynote talk at the 2019 Festival of Genomics, London.

The Festival of Genomics in London is a popular annual conference that attracts a multitude of diverse stakeholders from academia and industry.

On the one hand, this conference is a great forum for sharing details of the latest technological advances in the fast-moving field of genomics.

On the other hand, there is always a strong emphasis at this conference on issues that relate to the challenges of managing and sharing genome data from patients.

This includes ensuring that the staff who work in healthcare systems are properly equipped to be able to understand the basic science behind genomics so they can help address questions from patients.

This year’s conference featured several presentations from scientists at The Institute of Cancer Research. As cancer is a genetic disease it is not surprising that cancer researchers want to stay on top of the latest developments in this field.

The 100,000 Genomes Project

The opening keynote to the conference was given by Professor Mark Caulfield, the Chief Scientist at Genomics England. This is the organisation that was tasked with the mission to deliver the ground-breaking 100,000 Genomes Project.

As the name suggests, this project – which has profound implications for cancer research – aimed to decode the genetic blueprints of 100,000 genomes. But it is important to note that this does not mean that 100,000 people were involved.

Of the 103,311 genomes sequenced to date, almost a quarter (23,477) are cancer genomes. Some of the biggest benefits of this project will come from comparing pairs of matched genomes from the same patient.

Comparing a genome sequence from a tumour cell with one from a healthy cell allows researchers to pinpoint the genetic changes that are involved in causing cancer. Knowing the causes of cancer opens the door to developing new and improved treatments.

Professor Caulfield revealed that 50 per cent of 5,700 patients involved in the study have had a ‘known actionable’ or ‘partially actionable’ gene identified. These are the genes which can potentially be targeted, directly or indirectly, by a drug or other treatment.

He also recognised that although only 5 per cent of cancer patients are currently getting into a clinical trial, the 100,000 Genomes Project is helping expand the number of cancer patients who can get into trials.

To help make genomic medicine a reality for patients, the 100,000 Genomes Project has been supported by the development of the NHS Genomic Medicine Service. This is not only intended to benefit those patients who have their genomes sequenced but the data from the project – after being de-identified – is also being made available to academia and industry to aid research.

Concluding his talk, Professor Caulfield remarked: “Cancer is a really dramatic moment in life. If we can change this, we must take this opportunity.”

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Beyond 100,000 genomes

Although Professor Caulfield recapped several impressive statistics about the project to date – e.g. over 85,000 participants, 21 petabytes of data generated, 1,500 NHS staff involved, 3,000 researchers and trainees worldwide – the focus of his talk was very much about what comes next.

The new goal is for 500,000 whole genomes to be sequenced from the NHS in the next 5 years with a further ambition – recently revealed by the Health and Social Care Secretary Matt Hancock – to sequence five million genomes in the UK.

Although there are few governments around the world that have been as ambitious with plans to implement genome sequencing as part of routine healthcare, the UK is not alone.

A talk by Dr Xosé Fernández, Chief Data Officer Insitut Curie in Paris, provided an update on the Plan France Médicine Génomique 2025 project.

The goal of this project is to also sequence 500,000 genomes by 2025, with 175,000 cancer patients involved by the end of the project.

During his presentation, he presented the sobering statistics that more than 3.5 million people in Europe have been diagnosed with cancer, and between 1995 and 2012 the incidence has increased by 31 per cent.

Storing, distributing, and managing healthcare data is a key challenge of these type of projects and Dr Fernández also revealed that a particular challenge is the management of imaging data (such as from PET scans and mammograms) which accounts for 60 per cent of the data stored at Institut Curie.

The genomics of childhood cancer

The keynote on the second day of the conference was given by Professor Dame Sue Hill, the Chief Scientific Officer for NHS England.

Professor Hill was bullish on the NHS strategy for genomics, commenting that it will provide “an unparalleled resource with the NHS working alongside academia, industry, and others”.

She reiterated a point from the recently announced NHS Long Term Plan, that from 2019 all children with cancer will be offered whole genome sequencing to enable more comprehensive and precise diagnosis and access to more personalised treatment.

This is an issue that the ICR has been campaigning for and we welcomed this aspect of the Long Term Plan when it was announced earlier this month.

Professor Hill also recognised the need to do more for testing cancer predisposition genes, e.g. BRCA, and that there will be an enhanced focus on this area in the next few years.

 

How is the ICR adapting to this changing landscape?

Improving our understanding of cancer genomes is incredibly important to researchers at the ICR. Last year we became the first institute in the UK to implement Illumina’s ‘NovaSeq’ genome sequencing technology, which lets our researchers dramatically increase our ability to decipher the genetic code of tumours.

I spoke to Dr Nik Matthews, Genomics Manager of the ICR’s Tumour Profiling Unit, at the conference and asked him whether the ICR is ready to meet the challenge of ever-increasing amounts of cancer genome data, and he provided me with an upbeat assessment:

“The ICR is fantastically positioned to look at genomics data. We have our own scientific computing facilities and we have skilled researchers that work with big data all of the time. I believe that we are one the best-positioned institutes in England, if not in Europe, for this sort of data set”.

I look forward to attending next year’s conference to find out more about how genomics is revolutionising cancer research and about how the ICR is using this wealth of data to improve how we detect and treat this disease.

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