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Genomics England, NHS to Lead £105M UK Study with Aim to Sequence 100K Newborns


NEW YORK – The UK Department of Health and Social Care announced this week that it will invest £175 million (about $215 million) in genomic research, made in part to fulfil the goals of the country's Genome UK national genomic healthcare strategy, announced in September 2020.

Of the funding, £105 million will support a research study to improve the diagnosis of rare genetic diseases in newborns. The UK government said it will also invest £26 million to support cancer genomics research, and an additional £22 million to improve genomic data diversity.

Genomics England will lead the newborn screening study in partnership with the UK's National Health Service. The investigators' aim is to assess the effectiveness of using whole-genome sequencing to find and treat rare conditions in infants. As part of the Newborn Genomes Program, which will commence next year, about 100,000 newborns will be sequenced. Based on the outcome of the study, UK policymakers will then decide if it makes sense to introduce whole-genome sequencing of newborns across the country as part of routine care for infants.

Richard Scott, chief medical officer of Genomics England, said in a press briefing this week that the publicly funded company had not yet determined what sequencing platforms it will use in the Newborn Genomes Program when asked by this publication.

"We are working through the right approach, both in terms of technology and, for example, location of instruments and so on, but that is something we haven't yet fixed on," said Scott. He added that Genomics England currently relies on short-read and long-read genome sequencing technologies, with its "mainstay for rare disease diagnostics" being short-read technologies.

Genomics England and Illumina announced a deal in January 2020 to sequence 300,000 people in the UK, with a specific focus on rare diseases and cancer. Under the terms of that agreement, Illumina would sequence the samples in its Cambridge, UK-based facility using the NovaSeq 6000.

Scott made clear in the call though that the sequencing setup for the Newborn Genomes Program is "something we are working through" and said Genomics England will discuss it further once it "works through the right model and the right approaches over the next months."

Recruitment for the program, he noted in the briefing, should start by the end of 2023. It will carry on for two years, and then the investigators will start reporting back research findings. Ultimately, it will be up to the NHS to look at the evidence and decide if whole-genome sequencing is adopted. Scott underscored that the program is at this point just a research study.

"This is a complex area, there are a lot of questions, and we feel the right approach is to take a conservative approach," said Scott.

The current routine newborn screening test in the UK is the heel prick blood test, which is used to detect nine rare conditions, such as sickle cell disease and cystic fibrosis using a variety of approaches including mass spectrometry and immunoassays. Yet the opportunity to screen an infant's whole genome and uncover multitudes of conditions that might be treatable at an early stage is an attractive proposition to policymakers, who would like to shorten the time between when a patient becomes symptomatic and is eventually diagnosed with a genetic condition.

Scott noted that such diagnostic odysseys "put pressure" on the UK's health system, and said the new study is part of an effort to deal with the challenge. "This is a research study asking the question if this is something we should do and, if so, how," said Scott. "If it should, there could be enormous potential," he added.

Indeed, investigators believe the Newborn Genomes Program will pay off in the longer term, as they will be able to correlate the data gathered at birth with conditions developed later in life. As part of the program, Genomics England and the NHS said in a press briefing that they anticipate looking at about 200 conditions and that they estimate that about 3,000 children could be helped by such an approach, if adopted annually. About 680,000 children were born in the UK in 2020.

The initial focus of the Newborn Genomes Program will be England, Scott said during the briefing, though the investigators are in discussions with the devolved nations of Northern Ireland, Scotland, and Wales. Initially, it will launch within a handful of NHS trusts and then expand to cover roughly 30 health providers across the country, selected to represent diversity, both in the communities covered, as well as the environment in which they live, such as urban versus rural communities. Altogether, there are 219 NHS trusts in the UK providing healthcare.

Both NHS Wales and NHS England have rolled out whole-genome sequencing services for critically ill patients and those born with a disease, such as cancer, in recent years. These services however do not overlap with the new Newborn Genomes Program, which will recruit patients prior to birth, and will not be tested as part of routine care for critically ill infants.

Cancer 2.0 and Diverse Data

The remainder of the £175 million investment will support several other programs, including one focused on cancer research and another to improve the diversity of the UK's National Genomic Research Library. The government has also allocated £25 million to support UK Research and Innovation and Medical Research Council funding for functional genomics.

To support cancer research, the UK government will invest £26 million to support a program led by Genomics England and the NHS to evaluate the use of genomic sequencing in diagnosing cancer, as well as the integration of other kinds of data, such as imaging data combined with artificial intelligence, to improve cancer diagnosis and treatment.

Genomics England is in the midst of building a new cancer research program, called Cancer 2.0. As part of the effort, Genomics England is working with the National Pathology Imaging Cooperative to complete the processing of about 300,000 images from 16,000 participants in the 100,000 Genomes Project by mid-2023, which will be combined with AI tools and a variety of omics data. All of this data will then be used to provide faster, more accurate cancer diagnosis.

In addition to the funding for the Newborn Genomes Program and Cancer 2.0, the UK government also plans to invest £22 million to support the sequencing of up to 25,000 research participants of non-European ancestry and other populations who are underrepresented in the UK's National Genomic Research Library.

Again led by Genomics England, the investigators hope it will both reduce healthcare inequality, while improving their understanding of how genetic diversity might impact health outcomes. Such potential groups include those with sickle cell disease who tend to be of African ancestry.

Researchers from Genomics England have been working to improve data diversity in recent months, recently launching Link23, a new project aimed to address bias in genomics toward European populations.