Comparison of Circulating Tumour DNA and Extracellular Vesicle DNA by Low-Pass Whole-Genome Sequencing Reveals Molecular Drivers of Disease in a Breast Cancer Patient.

Olivia Ruhen,Carlos Salomon,Michael E Clark,Katie Meehan,Wendy Erber,Bella Nguyen,Bob Mirzai

doi:10.3390/biomedicines9010014

Abstract

There is increasing recognition of circulating tumour DNA (ctDNA) as a non-invasive alternative to tumour tissue for the molecular characterisation and monitoring of disease. Recent evidence suggests that cancer-associated changes can also be detected in the DNA contained within extracellular vesicles (EVs). As yet, there has been limited investigation into the relationship between EV DNA and ctDNA, and no studies have examined the EV DNA of breast cancer patients. The aim of this study was to use low-pass whole-genome sequencing to identify copy number variants (CNVs) in serial samples of both ctDNA and EV DNA from a patient with breast cancer. Of the 52 CNVs identified in tumour DNA, 36 (69%) were detected in at least one ctDNA sample and 13 (25%) in at least one EV DNA sample. The number of detectable variants in ctDNA and EV DNA increased over the natural history of the patient’s disease, which was associated with progression to cerebral metastases. This case study demonstrates that, while CNVs are detectable in patient EV DNA, ctDNA has greater sensitivity than EV DNA for serial monitoring of breast cancer.

Highlights

Copy number variants (CNVs) are among the most prevalent genomic alterations in breast cancer, with certain copy number variants (CNVs) such as the amplification of ERBB2 or the loss of heterozygosity at the BRCA1/2 loci associated with particular clinical phenotypes [1,2,3]
Recent data have indicated that cancer-related CNVs can be detected in the DNA of cancer patient-derived extracellular vesicles (EVs), which are membrane-bound vesicles released from a wide range of cells including tumour cells via exocytosis or membrane budding [7,8,9,10,11,12]
This case study is significant as it demonstrates that CNVs reflecting the tumour genomic profile can be detected in both the circulating tumour DNA (ctDNA) and EV DNA of a breast cancer patient

Summary

Introduction

Copy number variants (CNVs) are among the most prevalent genomic alterations in breast cancer, with certain CNVs such as the amplification of ERBB2 or the loss of heterozygosity at the BRCA1/2 loci associated with particular clinical phenotypes [1,2,3]. Whole-genome sequencing (WGS) of patient tumours has facilitated the discovery of a huge array of CNVs across the breast cancer genome; molecular profiling of tumour tissue is limited by sampling bias, tumour heterogeneity and lack of sample availability upon the emergence of metastatic lesions [1,4]. Circulating tumour DNA (ctDNA), small fragments of DNA that have been released into the circulation by apoptotic tumour cells, represents a potential surrogate for tumour tissue that can be sampled non-invasively to track clonal evolution and therapeutic response [4]. Low-pass WGS (LP-WGS) studies of ctDNA in breast cancer have determined that CNVs associated with metastatic progression and treatment response can be observed longitudinally throughout patient treatment [5,6]. There have been no studies investigating the utility of EV DNA for copy number profiling in breast cancer patients

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