Whole genome sequencing aids diagnosis and treatment for children with cancer in Cambridge University Hospitals study
The value of whole genome sequencing to speed up and improve diagnosis has been demonstrated in a pilot study involving 36 children treated for cancer at Cambridge University Hospitals NHS Foundation Trust.
The study was part of the 100,000 Genomes Project, which is designed to help create a new genomic medicine service for the NHS. The project was established to sequence 100,000 genomes from around 85,000 NHS patients affected by a rare disease or cancer.
Whole genome sequencing is the comprehensive method of analysing the full DNA code of your subject, giving a high resolution, base-by-base view. It shows up both large and small genetic differences, or variants, that might be missed by more targeted, next-generation sequencing approaches.
The Addenbrooke’s study involved 36 children with 23 different tumour types. Samples of their blood and tumour were sent to the lab for analysis.
Dr Patrick Tarpey, lead scientist for solid cancer in the East Genomic Laboratory Hub, based at Cambridge University Hospitals (CUH) NHS Foundation Trust, presented the findings at the National Cancer Research Institute (NCRI) Festival.
He said: “Whole genome sequencing can sometimes unravel unexpected results that may not have been considered via routine investigations. We’ve already learned a lot about using this type of test in our pilot study, both in terms of its benefits for children and in terms of how to get the best results.”
He revealed the process revealed several potentially important variants. In two cases, the information refined children’s diagnosis, while in four it changed their diagnosis. In eight cases, it revealed new information about their prognoses – the likely course of their disease.
In two cases, it showed possible hereditary causes of the cancers, while in seven others it suggested treatments that might not have been considered but were likely to be effective for treating the children.
In one of the seven cases, scientists found that two genes had become stuck together in a process known as gene fusion, which was probably encouraging the tumour to grow. Doctors used this knowledge to prescribe a different treatment involving an MEK inhibitor that would not normally be used to treat this type of cancer.
Dr Tarpey said: “Our results from this relatively small pilot group of children with cancer show how diagnosis and treatment can be improved.
“It suggests that offering whole genome sequencing to all children with cancer will provide more accurate diagnosis and prognosis, show whether there could be any hereditary cancer risk and help improve treatment options.”
The study also indicated that some of the important variants were difficult to spot among the wealth of data provided by whole genome sequencing. It was thanks to careful analysis and interpretation by an expert Genomic Tumour Advisory Board that they were not missed.
Dr Tarpey added: “As we scale up whole genome sequencing to complement current standard-of-care testing for children with cancer, we need to ensure we optimise all the steps in this process to reduce turnaround times and keep costs down.”
Dr Amos Burke, a consultant paediatric oncologist at CUH, said: “Being able to offer whole genome sequencing to all families of a child with cancer is a major step forward in allowing us to make the best diagnosis and to deliver the best treatment.
“We will continue to discover more that can help to cure childhood cancer, and as this new approach rolls out across the country, we look forward to seeing this as ‘standard-of-care’ for all children with cancer wherever they live.”
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