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

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 o...

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Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130429/
https://www.ncbi.nlm.nih.gov/pubmed/34006333
http://dx.doi.org/10.1186/s13073-021-00899-7
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-021-00899-7.

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