Title: Analysis of circulating tumour DNA (ctDNA) in patients with glioblastoma leveraging samples collected in the PARADIGM trial
Funder: Cancer Research UK

Abstract: Background Glioblastoma is a type of brain cancer with very poor prognosis, which currently has limited treatment options. To help find new effective treatments, novel biomarkers are required to monitor tumour burden before and after treatment. Circulating tumour DNA (ctDNA) has potential as a highly specific biomarker, enabling the detection of tumour-specific DNA in the plasma of cancer patients. ctDNA is currently in clinical use, most notably for the detection of EGFR mutations in non-small cell lung cancer, but published work has thus far shown only low detection rates of ctDNA in patients with glioblastoma. Aims This project aims to find an effective way to monitor glioblastoma by detecting ctDNA in patient plasma samples. Specifically, our objectives are to: •Assess the detection rate of ctDNA in a cohort of GBM patients •Assess the effects of radiotherapy (RT) alone, and in combination with the PARP inhibitor olaparib, on ctDNA in GBM patients •Correlate ctDNA detection with clinical outcomes Methods The proposed project is a feasibility study aiming to detect ctDNA in patients with glioblastoma using tumour and plasma samples from a clinical trial which is currently recruiting (PARADIGM, ISRCTN51253312). PARADIGM is a placebo-controlled Phase II study investigating the addition of olaparib, a PARP inhibitor, to radiotherapy, in patients who would otherwise receive radiotherapy alone. Plasma samples will be collected at several timepoints before and during radiotherapy treatment, and at disease progression. The research project will use next generation sequencing technology, and apply TAPAS, or TAilored PAnel Sequencing, which is a highly sensitive technique developed by the Rosenfeld Lab at Cancer Research UK Cambridge Institute to detect low levels of ctDNA, in the range of parts-per-million. Exome sequence analysis of patients’ tumours will be used to identify somatic mutations and design hybrid capture panels targeting patient-specific and common mutations found in glioblastoma. This panel will be sequenced to high depth to identify mutations in plasma in ctDNA. The project will also test the feasibility of using shallow whole genome sequencing to analyse fragmentation patterns of ctDNA and a circulating tumour mitochondrial DNA assay to improve detection of ctDNA. How this research will be used In the short term, the data generated will be used to assess feasibility for a larger scale analysis of the samples from the PARADIGM cohort and support an application for a PhD fellowship. In the longer term, the research aims to find an effective biomarker for glioblastoma.

Lay abstract: Background Glioblastoma is a type of brain cancer with very poor prognosis, which currently has limited treatment options. To help find new effective treatments, novel biomarkers are required to monitor tumour burden before and after treatment. Circulating tumour DNA (ctDNA) has potential as a highly specific biomarker, enabling the detection of tumour-specific DNA in the plasma of cancer patients. ctDNA is currently in clinical use, most notably for the detection of EGFR mutations in non-small cell lung cancer, but published work has thus far shown only low detection rates of ctDNA in patients with glioblastoma. Aims This project aims to find an effective way to monitor glioblastoma by detecting ctDNA in patient plasma samples. Specifically, our objectives are to: •Assess the detection rate of ctDNA in a cohort of GBM patients •Assess the effects of radiotherapy (RT) alone, and in combination with the PARP inhibitor olaparib, on ctDNA in GBM patients •Correlate ctDNA detection with clinical outcomes Methods The proposed project is a feasibility study aiming to detect ctDNA in patients with glioblastoma using tumour and plasma samples from a clinical trial which is currently recruiting (PARADIGM, ISRCTN51253312). PARADIGM is a placebo-controlled Phase II study investigating the addition of olaparib, a PARP inhibitor, to radiotherapy, in patients who would otherwise receive radiotherapy alone. Plasma samples will be collected at several timepoints before and during radiotherapy treatment, and at disease progression. The research project will use next generation sequencing technology, and apply TAPAS, or TAilored PAnel Sequencing, which is a highly sensitive technique developed by the Rosenfeld Lab at Cancer Research UK Cambridge Institute to detect low levels of ctDNA, in the range of parts-per-million. Exome sequence analysis of patients’ tumours will be used to identify somatic mutations and design hybrid capture panels targeting patient-specific and common mutations found in glioblastoma. This panel will be sequenced to high depth to identify mutations in plasma in ctDNA. The project will also test the feasibility of using shallow whole genome sequencing to analyse fragmentation patterns of ctDNA and a circulating tumour mitochondrial DNA assay to improve detection of ctDNA. How this research will be used In the short term, the data generated will be used to assess feasibility for a larger scale analysis of the samples from the PARADIGM cohort and support an application for a PhD fellowship. In the longer term, the research aims to find an effective biomarker for glioblastoma.

Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS