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

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

Onderzoeksoutput: Bijdrage aan tijdschriftArtikelpeer review

5 Citaten (Scopus)

Samenvatting

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.

Originele taal-2Engels
Artikelnummer86
TijdschriftGenome Medicine
Volume13
Nummer van het tijdschrift1
DOI's
StatusGepubliceerd - dec. 2021

Vingerafdruk

Duik in de onderzoeksthema's van 'Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients'. Samen vormen ze een unieke vingerafdruk.

Citeer dit