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Genomics England Partners With Sectra to Combine Genomics, Digitized Medical Imaging Data


NEW YORK – Genomics England recently installed Sectra's imaging system for managing radiology and pathology imaging data, enabling it to access medical images from more than 30 UK National Health Service hospital trusts. The British company aims to combine the digital pathology and radiology data with its whole-genome sequencing dataset to create a new cancer multimodal research platform.

According to Prabhu Arumugam, director of clinical data and imaging at Genomics England, the firm has short- and long-term plans for this emerging data resource but has already given some early users both in industry and academia access to it. At first, research will be focused on correlating well-known cancer-associated variants, such as HER2, to relevant imaging data collected from patients. A hope is that by combining imaging and genomics in the future, clinicians will be able to improve diagnoses and make more informed decisions about therapies.

"It's going to take a few years to understand the dataset in its entirety," said Arumugam, who is a pathologist by training.

Genomics England's current plans are to start looking at validated cancer biomarkers. Going forward, researchers could track disease progression as captured via magnetic resonance imaging, retrospectively review any changes in their DNA, and then use both data sources to inform new diagnostics.

"It gets really interesting in that we can make this useful for oncologists and individual patients," remarked Arumugam. "It will be a big step for us and the cancer community."

Based in Linköping, Sweden, Sectra has long provided its Image Exchange Portal to the UK's National Health Service. At its core, the system has a vendor neutral archive, which enables users to consolidate a variety of imaging data in one place. To facilitate the transfer of NHS pathology and radiology images to Genomics England, the company decided to have a Sectra system installed last year, and the installation was completed last month. The amount of the associated contract was not disclosed. With the installation of the Image Exchange Portal complete, Genomics England has begun linking its own whole-genome sequencing data with imaging data obtained from the NHS to build its platform.

According to Arumagam, 32 NHS trusts will provide data on solid tumors using the Sectra Image Exchange Portal. A trust is a unit of the NHS that serves a particular geographical region or is specialized in some way. Genomics England will be able to access about 250,000 pathology images and 200,000 radiology scans for 16,000 participants in its cancer cohort. All of the images are being digitized and de-identified for analysis by the National Pathology Imaging Co-operative (NPIC), a UK initiative to digitize pathology images that commenced last year.

Once the radiology and pathology data in the system is matched with the genomics data, multimodal data will be used by researchers to investigate and identify markers for cancer diagnostics and treatments. To protect the identities of participants, researchers outside of Genomics England will only be able to access an identification number, the participant's age, and the name of the site where the data was collected.

Arumugam noted that the Sectra system is installed on the Amazon Web Services cloud, which will allow Genomics England to scale its own research efforts, as well as to give more investigators access to the genomics, pathology, and radiology data, potentially leading to new discoveries that could impact clinical care. Currently, only a handful of users have access to the data, though Genomics England plans to onboard about half-dozen more in coming months.

The scans themselves provide insight into disease progression, from diagnosis through surgery and chemotherapy, Arumugam noted, meaning that researchers can see how tumor sizes correlate to treatment. "We can ask if there is a correlation between genomic markers and what we see in the scans," he said. Arumugam cautioned that it will take a year or two before researchers are able to understand genomics data in the context of longitudinal disease progression.

Genomics England is inarguably one of the premier genomics research organizations globally, founded a decade ago to oversee the 100,000 Genomes Project. Arumugam joined the company three years ago to oversee its extension into medical imaging as part of an effort to build a multimodal dataset for cancer research.

While deployment of genomics in the UK healthcare system continues, notably through the NHS Genomic Medicine Service, Arumugam said that the rollout of digital pathology in the UK is "still in its infancy," though he credited NPIC with educating pathologists about new platforms, as well as providing some with scanners. The country has been investing in both AI and digital pathology, and in 2018, it invested £50 million ($64 million) to support five centers across the UK.

The development of these new technologies, however, have concerned some radiologists and pathologists who fear that artificial intelligence-based tools developed from resources such as the new multimodal dataset could reduce the need for their work, though Arumugam stressed this isn't the case.

"We see this as a research asset, and it will take time to understand its value," said Arumugam. Instead, the data will more likely be used at first to support therapeutic decisions, as well as for clinical diagnostics, he said.

"That is where we would like this dataset to help clinicians, academics, pharma, and industry," said Arumugam, "to expedite their knowledge and to expedite [the development of] their tools."

According to Sectra CEO Torbjörn Kronander, his company's partnership with the NHS goes back decades. The company last year announced deals with the East Suffolk and North Essex NHS Foundation Trust and the West Suffolk NHS Foundation Trust, for instance.

"We have a large presence in the UK with a lot of customers in the NHS," he said. For the new partnership with Genomics England, the company will provide cloud-based data storage and management services, which given the size of both genomics and imaging data, can be challenging.

Konander said that the relationship with Genomics England is "important" for Sectra, as it will allow the Swedish firm to learn from one of the largest cohorts in the world. "We hope this can be a partnership that we can develop in the future," he said.

Sectra has experience in making its imaging platform useful for genomics researchers and last year created a new business unit focused on genomics, which he said in a statement at the time fits with the company's ambition to be a "leader in diagnostics information technology." At that time, Sectra also initiated a collaboration with scientists at the University of Pennsylvania around developing systems to manage both genomics and imaging data.

"We do have a lot of experience dealing with genomics data," said Kronander. "Molecular pathologists want to know where the sequencing data is coming from in a specimen," he said. "It could be germline DNA or somatic DNA, and we can help them answer those questions."

Kronander said that the features Sectra is developing with its partners at the University of Pennsylvania have not been made available to Genomics England, but he said that they could be offered to the company in the future. Moreover, he stressed that the work that Sectra is doing with UPenn and Genomics England is part of a greater trend of industrializing healthcare.

"Industrialization might sound hard and cold but it's not," said Kronander. "It means repeatable quality at an affordable price, that care can be as good for a patient as possible and still be efficient for providers."

Getting there, however, will take time. For Genomics England, immediate goals are to have a digital library ready containing genomics, pathology, and radiology images available in the cloud. Arumugam also would like to have at least 10 users within Genomics England's multimodal cancer data environment this year. "Our big aims are to bring on the library, bring on early users, and drive diagnoses," he said.

Early users will also help Genomics England to identify what tools might be needed to help researchers navigate the dataset, Arumugam added. "What we will learn in the next year is how to make an end-to-end analysis pipeline," he said, "and how to make that platform usable and shareable."