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Genomics England Preps for NHS Genomic Medicines Service Launch With New Focus, Tools


NEW YORK – Genomics England is scaling up to support the full launch of the UK National Health Service's Genomic Medicines Service later this year.

The service will provide whole-genome sequencing to English patients with certain rare diseases and cancer as part of routine care, an offering that organizers say is the first of its kind in the world. The launch will also demonstrate Genomics England's transition from a company established to support the 100,000 Genomes Project to a national platform for clinical diagnostics and research.

"We decided to go from being a project organization to a platform organization," said Genomics England CEO Chris Wigley. "As a project organization, we built technology to get to a finish line. As a platform organization, we will enable an ecosystem for genomics in the UK."

Wigley took the helm of London-based Genomics England in October 2019. He joined the firm from QuantumBlack, a machine learning and artificial intelligence firm, where he served as chief operating officer, and he had prior experience as a diplomat with the British Foreign Office. His appointment came at a time when Genomics England was wrapping up the sequencing and analysis connected to the 100,000 Genomes Project, a "passion project," in Wigley's words, of then-Prime Minister David Cameron that commenced in July 2013 and was completed in December 2018.

To support that project, Genomics England was established in 2013 as a private company, wholly owned by the UK Department of Health and Social Care. It currently employs around 250 people. But with the project's aims met, it has looked for new ways to use its resources to support the uptake of genomics in UK healthcare.

Wigley said the new, repurposed Genomics England is now anchored on two services: the partnership with the NHS to support the rollout of the National Genomic Medicines Service, as well as making de-identified datasets, including whole-genome sequencing data, available for academic and industry researchers.

In terms of the NHS partnership, Genomics England will oversee the rollout of the service across England, "from Sunderland to Cornwall," though Genomics England will also support NHS Wales, NHS Scotland, and NHS Northern Ireland on an on-demand basis.

"For anyone in England, which is 57 million people, you will have equal access to this testing," said Wigley.

Whole-genome sequencing will be ordered via seven NHS England Genomic Laboratory Hubs (GLHs) across the country in Birmingham, Cambridge, Manchester, Bristol, Newcastle, and London, where there are two GLHs. The sequencing will be conducted in partnership with San Diego-based Illumina, which maintains a site in Cambridge, and the results will be reported back via the GLHs.

Data from this healthcare work, meantime, including genomic and clinical information, is being pooled into a data asset that Genomics England will make available to academics and industry.

"The use cases here are either fundamental academic research or target discovery for target development for biotechs and pharmas, or assessing diagnostic tools or companion diagnostics," Wigley said. "There are a range of research goals that people are interested in pursuing."

According to Wigley, most users of Genomics England's de-identified data so far, among them 3,600 academic researchers, have been in the UK, though some are in the US and Asia. The cohort includes 130,000 whole genomes from the 100,000 Genomes Project, but it will grow in coming years as new genomes are delivered via the National Genomic Medicines Service, with the consent of patients.

Industry can access the environment on commercial terms, Wigley said. He noted that Genomics England also maintains a biobank of 36,000 blood samples for resequencing and other necessary assays, plus the ability to recontact participants. This is particularly useful for companies developing therapies for rare diseases, where there might be only a dozen or so people in the UK with a certain condition, he added.

In June 2020, Genomics England also announced a partnership with Amazon Web Services and technology firm Lifebit to create a new genomic research environment supported by AWS's cloud computing and storage infrastructure. Wigley said that Genomics England previously had stored data on an in-house server called UK Cloud, but that the partnership with AWS and Lifebit was necessary to scale for future use by a potentially large group of users.

"We have lots of users running big jobs," said Wigley. "We had to schedule those in the past because of finite resources, but now we can scale that in the cloud, which is really helpful."

Genomics England is also considering consolidating data assets from the UK Biobank, a repository of genotyping and sequencing data on 500,000 British participants, as well as the European Bioinformatics Institute into a single searchable research environment, Wigley said. EBI is headquartered at the Wellcome Trust Genome Campus in Hinxton, outside Cambridge.

"We are trying to get to a point where we can federate some of those datasets across multiple front ends, so we have some common shared data assets that are accessible with the right approvals from those data portals," said Wigley.

Genome UK

Genomics England's activities support Genome UK, the country's first national genomic healthcare strategy. The government unveiled the 64-page report last September, pledging to deliver to patients better clinical care, and setting whole-genome sequencing at the heart of its aims.

Specifically, the report highlighted the rollout of the NHS England Genomics Medicine Service as what they described as the first in the world to offer whole-genome sequencing as part of routine care. The report also cited the implementation of pharmacogenomics to better select drug treatments, as well as bundling genomic, imaging, and longitudinal healthcare data to better treat cancer patients, as milestones for achieving the strategy.

Wigley noted that the UK has had previous strategies and reports that focused on genomics, such as the Generation Genome 2016 Report, yet none have provided as comprehensive a strategy as Genome UK.

"What we tried to do with the strategy is outline how the ecosystem works, what we are trying to achieve, what the shared elements of that are," he said. "What this is doing is drawing out and double-clicking on all the genomics activities in this space."

As such, he described the launch of the NHS Genomics Medicine Service as important for achieving the Genome UK goal, describing it as a "landmark moment."

Illumina partnership

In early 2020, Genomics England partnered with Illumina to deliver 300,000 whole genomes by 2025. According to Clare Kingsley, senior director of scientific research at the company, whole-genome sequencing connected to Genomics England is performed by Illumina Laboratory Services in Cambridge, the same lab that delivered sequencing for the 100,000 Genomes Project.

"Illumina continues to support the NHS and Genomics England in their efforts to position England as a global leader in genomics," Kingsley said in an email. She underscored that with the launch of the NHS Genomic Medicines Service, the UK will become the "first healthcare system in the world to adopt whole-genome sequencing into clinical practice."

She reiterated that the service will initially serve patients with certain rare and undiagnosed genetic diseases and cancer, and that all genomes will be generated using Illumina's NovaSeq 6000 platforms and complementary bioinformatics analysis tools.

"As the benefits of whole-genome sequencing in clinical care are realized, we anticipate an expansion in the number of clinical indications included in the [UK] National Genomic Test Directory," predicted Kingsley. "Genomic insights will continue to facilitate more rapid and precise diagnoses, provide more effective and tailored treatment options, and improve patient outcomes."

Kingsley also noted the cooperation with Genomics England is a step toward achieving the NHS Long Term Plan, which calls for a widened role for genomics in clinical care. "Through this partnership, other applications for whole-genome sequencing in healthcare will be explored," she said.