Rapid identification of somatic genome rearrangements as personalized biomarkers for blood-based cancer monitoring

Study ID Alternative Stable ID Type
EGAS00001003963 Other

Study Description

Increasing evidence shows the value of circulating tumour DNA (ctDNA) to detect cancer and monitor its progression. Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of ctDNA in liquid biopsies. However, accurate, affordable, and fast identification of such SV biomarkers is challenging, which hinders routine use in the clinic. Here, we demonstrate a novel approach - termed SHARC - for rapid discovery of somatic SV breakpoints as personalized tumour biomarkers. SHARC combines low-coverage cancer genome sketching by using Oxford Nanopore portable sequencing with a random forest classification and a dedicated filtering pipeline to enrich for somatic SVs. Our method leverages the real-time and long-read capabilities of Nanopore sequencing to identify somatic SV breakpoints at nucleotide resolution from a tumour biopsy within two days. We applied SHARC to tumour samples of high-grade ovarian and prostate cancer and validated on average 10 somatic SVs per sample with the use of PCR mini-amplicons. Finally, we demonstrate ... (Show More)

Study Datasets 2 datasets.

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Dataset ID Description Technology Samples
Low coverage nanopore sequencing of ovarian cancer tumors
GridION,MinION 4
Low coverage nanopore sequencing of prostate cancer tumors
GridION 5

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