Scientists create “metal detector” to hunt down tumours

The algorithm could one day help doctors figure out which patients are more likely to have successful treatment.

That could pave the way for more personalised treatment plans that increase people’s chances of survival.

Professor Serena Nik-Zainal, is Professor of Genomic Medicine and Bioinformatics at the University of Cambridge.

The researcher said: “Genomic sequencing is now far faster and cheaper than ever before.

“We are getting closer to the point where getting your tumour sequenced will be as routine as a scan or blood test.

“To use genomics most effectively in the clinic, we need tools which give us meaningful information about how a person’s tumour might respond to treatment.

“This is especially important in cancers where survival is poorer, like lung cancer and brain tumours.

“Cancers with faulty DNA repair are more likely to be treated successfully.

“PRRDetect helps us better identify those cancers and, as we sequence more and more cancers routinely in the clinic, it could ultimately help doctors better tailor treatments to individual patients.”

The research team looked for patterns in DNA created by so-called “indel” mutations, in which letters are inserted or deleted from the normal DNA sequence.

They found unusual patterns of “indel” mutations in cancers which had faulty DNA repair mechanisms – known as “post-replicative repair dysfunction” or PRRd.

Using this information, the scientists developed an algorithm called PRRDetect which allows them to identify tumours that have PRRd from a full DNA sequence.

PRRd tumours are more sensitive to immunotherapy, a type of cancer treatment that uses the body’s own immune system to attack cancer cells.

The scientists hope that the PRRd algorithm could act like a “metal detector” to allow them to identify patients who are more likely to have successful treatment with immunotherapy.

The study follows from a previous “archaeological dig” of cancer genomes carried out by Professor Serena Nik-Zainal and funded by Cancer Research UK.

This “dig” examined the genomes of tens of thousands of people and revealed previously unseen patterns of mutations which are linked to cancer.

This time, Professor Nik-Zainal and her team looked at cancers which have a higher proportion of tumours with PRRd.

These include bowel, brain, endometrial, skin, lung, bladder and stomach cancers.

Whole genome sequences of these cancers were provided by the 100,000 Genomes Project – a pioneering study led by Genomics England and NHS England which sequenced 100,000 genomes from around 85,000 NHS patients affected by rare diseases or cancer.

The study identified 37 different patterns of indel mutations across the seven cancer types included in this study.

Ten of these patterns were already linked to known causes of cancer, such as smoking and exposure to UV light. Eight of these patterns were linked to PRRd.

The remaining 19 patterns were new and could be linked to causes of cancer that are not fully understood yet or mechanisms within cells that can go wrong when a cell becomes cancerous.

Executive Director of Research and Innovation at Cancer Research UK, Dr Iain Foulkes, said:

“Genomic medicine will revolutionise how we approach cancer treatment. We can now get full readouts of tumour DNA much more easily, and with that comes a wealth of information about how an individual’s cancer can start, grow and spread.

“Tools like PRRDetect are going to make personalised treatment for cancer a reality for many more patients in the future.

“Personalising treatment is much more likely to be successful, ensuring more people can live longer, better lives free from the fear of cancer.”