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

Author:

Valle-Inclan Jose Espejo,Stangl Christina,de Jong Anouk C.,van Dessel Lisanne F.,van Roosmalen Markus J.,Helmijr Jean C. A.,Renkens Ivo,Janssen Roel,de Blank Sam,de Witte Chris J.,Martens John W. M.,Jansen Maurice P. H. M.,Lolkema Martijn P.,Kloosterman Wigard P.ORCID

Abstract

AbstractHere, 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.

Funder

KWF Kankerbestrijding

Publisher

Springer Science and Business Media LLC

Subject

Genetics (clinical),Genetics,Molecular Biology,Molecular Medicine

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