Detecting clinically relevant mutations in circulating tumour DNA
Research type
Research Study
Full title
A targeted Next Generation Sequencing (NGS) approach to detect activating and resistance mutations in the circulating tumour DNA of cancer patients.
IRAS ID
242602
Contact name
Claire Faulkner
Contact email
Sponsor organisation
Research & Innovation, North Bristol NHS Trust
Duration of Study in the UK
1 years, 0 months, 1 days
Research summary
Research Summary
Cancer can be considered a genetic disease whereby changes in DNA, known as mutations, can drive the formation of tumours. It is possible to treat patients known to have specific mutations in their tumours with drugs which precisely target these mutations; this is known as personalised medicine. In order to determine if a patient’s tumour contains a specific mutation that is eligible for targeted treatment, surgical removal of tissue (a biopsy) for genetic testing is required. Often a successful biopsy may not be possible due to the wellbeing of the patient or the location of the tumour, preventing the testing required for the targeted treatment.
Another form of genetic testing which is derived from a blood sample, known as circulating tumour (ct) DNA testing can be used as an alternative to a biopsy. This was developed from the knowledge that tumours shed DNA into the blood stream. ctDNA, also known as a ‘liquid biopsy’ can be used to diagnose a particular cancer type which can determine the appropriate treatment, as well as monitoring response to treatment via changes in the levels of ctDNA in the blood and to screen for any resistance mutations the tumour may have evolved against the treatment.
The aim of this project is to use a technology known as next-generation sequencing (NGS), which can “read” the sequence of DNA, to detect clinically relevant mutations in the circulating tumour DNA (ctDNA) of cancer patients. There are two patient groups which will be recruited onto our study for the detection of mutations in their ctDNA; patients with lung cancer and patients with melanoma (skin cancer). The mutations found in patient’s ctDNA will be compared with those found in their tissue sample. We will examine if ctDNA testing can be used as a monitoring tool to detect resistance mutations.
Summary of Results
The aim of this project was to use a technology known as next-generation sequencing (NGS) to detect mutations in blood samples from cancer patients. The DNA present in the blood of cancer patients is called circulating tumour DNA (ctDNA). The detection of mutations in a blood sample is beneficial for cancer patients as it reduces the need for an invasive tissue biopsy. It also has the potential to be used as a monitoring tool to track disease and resistance to treatment. A sensitive technique is needed to detect mutations in blood as they are present at a low level.
A method to extract ctDNA from blood samples that is new to the laboratory was evaluated. This showed good extraction efficiency and suitability for downstream ctDNA mutation analysis.
A Next Generation Sequencing panel was validated using control reference materials at a range of mutation frequencies. The panel was shown to be able to detect mutations at low levels in blood samples (1% -5% mutation frequency) showing that it was suitable for ctDNA detection.
Five participants with known mutations were recruited to the study, four patients with lung cancer and one patient with melanoma. Of these, four patients were recruited to the monitoring group and one to the diagnostic group. In both groups, a blood sample was taken which was compared to a previous tissue sample to find out if the mutations detected in the tissue sample could also be detected in the blood sample. In the monitoring group, blood samples were also taken at two monthly intervals for a period of up to 6 months to find out if the mutation level or type changed during cancer treatment.
Comparing the matched tissue and blood samples using NGS showed that the mutations could be detected in the ctDNA sample in 57% of samples (4/7 mutations detected in blood versus tissue samples). This shows that NGS analysis can detect mutations in ctDNA samples from cancer patients, but analysis from blood samples is not as sensitive as tissue analysis.
In the monitoring group, a correlation between the patients’ clinical response to treatment and the mutation level in the blood was observed. This shows that ctDNA analysis has potential utility as a monitoring tool.
The emergence of a resistance mutation was observed in a blood sample from a lung cancer patient who was becoming resistant to tyrosine kinase inhibitor (TKI) therapy. This shows that NGS analysis of ctDNA samples can be used to detect resistance mutations.
This study has shown that NGS analysis of ctDNA samples has potential clinical utility for cancer patients.
REC name
London - Brighton & Sussex Research Ethics Committee
REC reference
18/LO/0966
Date of REC Opinion
1 Jun 2018
REC opinion
Further Information Favourable Opinion