Scientists use genomic sequencing to pinpoint cause of rare diseases

Hundreds of seriously ill patients in the UK suffering from undiagnosed conditions have had the underlying genetic causes pinpointed by a groundbreaking project, which scientists believe will cut the cost to the NHS of treating rare diseases and improve patient care.

First scientific results from the 100,000 Genomes Project, a £300m five-year initiative funded mainly by the UK government, were published in the New England Journal of Medicine on Wednesday.

Whole genome sequencing — reading all 3bn biochemical letters of each individual’s genetic code — made it possible to diagnose the underlying cause of rare diseases in 535 patients from the 2,183 families who participated in the early stages of the project.

The scientists said that three-fifths of the patients would have had their diagnosis missed by more conventional tests, including less advanced forms of genomic testing.

The UK leads the world in genomic sequencing and the researchers said it could unlock novel treatments for 3m Britons suffering from rare diseases and lead to big cost savings for the NHS. The pilot study analysed the genes of more than 4,600 people in total — patients and their families.

The study found that those who received a diagnosis from the study were able to benefit from “more focused clinical care”, including further family screening, dietary changes and other therapies.

Mark Caulfield, the former chief scientist at Genomics England, who launched the project in 2013, said the earlier, more accurate diagnosis enabled by whole genomic sequencing would speed up the path to treatments for patients.

He added that this would also save the health service money by reducing the need for regular hospital stays.

“Because this is part of repeated, ongoing care and these people are in and out of the system the whole time, they are using a lot of resource,” said Caulfield. “If we could focus that on getting the diagnosis, and that’s what we hope from this programme, then we can use less resource to monitor them and maybe move in some cases . . . to treatment.”

The patients in the study had more than 180,000 hospital visits at a combined cost of around £87m to the NHS.

One of the lead researchers, Damian Smedley, professor of computational genomics at London’s Queen Mary University, said a large proportion of the diagnoses “would not have been detected by existing approaches”.

The use of whole genome sequencing had helped “solve the ‘needle in a haystack’ challenge” of finding the cause of rare disorders, said Smedley. He called on healthcare systems worldwide to adopt whole genome sequencing.

For certain disease categories, including rare hearing or eye disorders and intellectual disabilities, genomic testing led to the successful diagnosis of more than 40 per cent of patients.

Dr Richard Scott, chief medical officer at Genomics England, said the study showed how genomic diagnostics can improve outcomes for patients with rare diseases as previously a diagnosis often involved “multiple different targeted tests — an approach that can delay diagnosis and access to more tailored care.”

Since it began, the project has analysed 100,000 genomes from people affected by rare diseases and various cancers and their relatives but has yet to analyse all the results. After the project was completed in 2018, the NHS adopted the techniques as part of its Genomic Medicine Service and has pledged to use them to sequence at least 300,000 genomes by 2025.