Community Research and Development Information Service - CORDIS

ERC

CancerExomesInPlasma Report Summary

Project ID: 337905
Funded under: FP7-IDEAS-ERC
Country: United Kingdom

Mid-Term Report Summary - CANCEREXOMESINPLASMA (Non-invasive genomic analysis of cancer using circulating tumour DNA)

Non-invasive genomic analysis of cancer has significant translational potential. Analysis of tumour DNA fragments that are shed into body fluids such as blood plasma, known as circulating tumour DNA (ctDNA), has been shown to allow monitoring of disease burden and emergence of treatment resistance. This also provides novel insights into tumour evolution and heterogeneity. The CancerExomesInPlasma project applies genome-wide analysis to ctDNA for broad and unbiased discovery of genes and pathways involved in resistance to systemic therapy. It generates technological and methodological development that will allow sensitive analysis of even small amounts of ctDNA such as are found in early stages of cancer or in patients harbouring minimal residual disease after treatment. The project will further support and generate new discoveries on the biology of cell-free DNA in plasma and other peripheral fluids such as urine and cerebral spinal fluid.

We have optimised sequencing protocols to sequence ctDNA at an exome scale, even when using as little as one nanogram of input DNA. We established a work-flow that allows us to study broad mutation profiles at high sensitivity. Whole-exome sequencing of patient samples with high levels of tumour DNA identifies tumour specific sequence alterations, from which we design personalised panels for deep sequencing. These are used for higher-sensitivity sequencing of samples including plasma collected at multiple time-points. This approach was applied to samples from patients with metastatic cancer, collected before and after targeted therapies. As well as providing data on mechanisms of treatment resistance, our findings suggest that analysis of plasma ctDNA can mitigate biased mutation detection in tumour biopsies.

We applied this approach to establish to what extent ctDNA can detect and characterise multifocal clonal evolution in a patient with metastatic breast cancer (Murtaza et al, Nat Commun 2015). We showed that ctDNA analysis is more likely to show “stem” mutations common to all cancer sites, but that levels of sub-clonal mutations that are “private” to individual lesions can reflect the varying responses of different lesions.

We develop our methodologies to study ctDNA in ever more challenging settings. For example, in early stages of cancer or after treatment, ctDNA levels can be very low such that a tube of blood might not contain a single copy of an individual pre-specified mutation of interest that may be found in the tumour cells. A further challenge arises from limitations and biases of DNA sequencing technologies, which generate noise and errors that can be mistaken for false positive signals. To address these challenges we combine novel approaches to reduce sequencing biases with multiplexed analysis of large numbers of mutations, to increase the likelihood that some mutations will be detected, even if average levels are extremely low.

Our studies provided insights in to the biology of cfDNA. Improved understanding allows us to tailor our methods for analysis of ctDNA to improve its utility as a cancer biomarker. For example, our work has generated strong evidence that ctDNA is shorter than cell-free DNA of non-tumour origin, supporting the notion that size-selection may allow enrichment of ctDNA to improve sensitivity of analysis.

Individually, and in combination, the above developments will improve the efficiency, sensitivity and specificity of ctDNA analysis using a variety of sequencing approaches, facilitating the on-going studies of tumour evolution in response to therapy and generating proofs of concept for an increasing range of clinical applications for ctDNA to aid in clinical diagnostics and management of cancer.

Reported by

THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom
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