Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

Abstract Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of hig...

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Bibliographic Details
Main Authors: Jose Espejo Valle-Inclan, Christina Stangl, Anouk C. de Jong, Lisanne F. van Dessel, Markus J. van Roosmalen, Jean C. A. Helmijr, Ivo Renkens, Roel Janssen, Sam de Blank, Chris J. de Witte, John W. M. Martens, Maurice P. H. M. Jansen, Martijn P. Lolkema, Wigard P. Kloosterman
Format: Article
Language:English
Published: BMC 2021-05-01
Series:Genome Medicine
Subjects:
Genomics
Liquid biopsies
Nanopore
Cancer
Structural variation
Online Access:https://doi.org/10.1186/s13073-021-00899-7
Description
Summary:Abstract Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons. These SVs could be quantified in ctDNA samples of patients with metastatic prostate cancer using a digital PCR assay. The results suggest that SV dynamics correlate with and may improve existing treatment-response biomarkers such as PSA. https://github.com/UMCUGenetics/SHARC .
ISSN:1756-994X

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