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UK Study Supports Use of Whole-Genome Sequencing in Standard Cancer Care

NEW YORK – The pairing of whole-genome sequencing and clinical data can yield actionable information to better guide treatment of cancer patients, and genomic sequencing should become routine for certain cancers in the UK, according to the authors of a new study.

Researchers from Genomics England, the National Health Service England, Queen Mary University of London, the University of Westminster, and Guy's and St Thomas' NHS Foundation Trust published their findings in Nature Medicine on Thursday.

The paper discusses their analysis of 33 types of solid tumors obtained from 13,800 participants in the UK's 100,000 Genomes Project. All of the tumors were sequenced at an average coverage of 100X on the Illumina HiSeq platform, while normal matches were sequenced at 30X for comparison. The researchers also looked at clinical data, such as hospital visits and prescribed treatments, as well as survival rates and patient outcomes.

In general, the researchers found that whole-genome sequencing yielded more comprehensive information than relying on cancer panels. They also made specific findings. Among those reported were that most brain cancers and more than half of colon and lung cancers showed genetic changes that could be used to guide future treatment. In sarcomas, about a tenth of tumors had structural variants that could be used for similar purposes.

The analysis also turned up genetic changes that could be linked to treatment response and to predict patient outcomes. They stated that the results support the increased adoption of whole-genome sequencing for cancer patients within the NHS Genomic Medicine Service, which NHS England in partnership with Genomics England introduced in 2018.

Nirupa Murugaesu, principal clinician in cancer genomics and clinical studies at Genomics England and corresponding author on the paper, discussed the findings in an online media briefing this week. She credited the 100,000 Genomes Project with laying the foundation for the cancer study, and whole-genome sequencing with being able to deliver a "comprehensive inventory" of genomic alterations, ranging from copy number alterations to pangenomic and pharmacogenomic markers, which was complemented by "longitudinal life course data" collected by NHS England.

"This is an example of where a single test was able to capture all of these different types of information and all of these different types of gene alterations," said Murugaesu. "Our findings supported the commissioning of whole-genome sequencing in a subset of cancers."

That subset is glioma, sarcoma, and high-grade serous ovarian cancer, testing for which is being delivered via seven genomics hubs in the UK. NHS England also offers whole-genome sequencing for all pediatric cancers, she noted, as well as for acute leukemias. "This is where there is a case for whole-genome sequencing," said Murugaesu, who is also an oncology consultant and cancer genomics lead at Guy's and St Thomas' NHS Foundation Trust in London.

For other cancers, the standard of care continues to involve the use of targeted cancer panels, though the researchers expect that to change over time. Genomics England CSO Matt Brown noted during the briefing that the cost of whole-genome sequencing continues to decline, which may influence how the technology is used by the NHS in the future.

Brown added that Genomics England is currently involved in a cancer research program, part of which involves assessing the utility of long-read sequencing platforms for testing leukemias, gliomas, and sarcomas. GEL is also developing a multimodal dataset that includes histopathology and imaging data from 100,000 Genomes Project participants and is being optimized for AI. He called this "a rich dataset" that will lead to the "next generation of analytic approaches for cancer."

Given these efforts, Brown said that Genomics England expects to see "further changes toward whole-genome sequencing and away from panels over time."