Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

Molecular Cancer

Filippo Martignano¹  Uday Munagala²  Silvestro G. Conticello³  Alessandra Mingrino⁴  Alberto Magi⁵  Roberto Semeraro⁶  Stefania Crucitta⁶  Marzia Del Re⁶  Iacopo Petrini⁷ 

[1] Core Research Laboratory, ISPRO, Florence, Italy;Department of Medical Biotechnologies, University of Siena, Siena, Italy;Core Research Laboratory, ISPRO, Florence, Italy;Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), University of Florence, Largo Brambilla 3, 50134, Florence, Italy;Core Research Laboratory, ISPRO, Florence, Italy;Institute of Clinical Physiology, National Research Council, Pisa, Italy;Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy;Department of Information Engineering, University of Florence, Florence, Italy;Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy;Unit of Respiratory Medicine, Department of Critical Area and Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa, Italy;

关键词: Copy number aberrations. Diagnosis;    Metastasis;    Plasma;    Third generation sequencing;    cfDNA;    ctDNA;    Circulating tumor DNA;   

DOI  :  10.1186/s12943-021-01327-5

来源: Springer

【 摘 要 】

In the “precision oncology” era the characterization of tumor genetic features is a pivotal step in cancer patients’ management. Liquid biopsy approaches, such as analysis of cell-free DNA from plasma, represent a powerful and noninvasive strategy to obtain information about the genomic status of the tumor. Sequencing-based analyses of cell-free DNA, currently performed with second generation sequencers, are extremely powerful but poorly scalable and not always accessible also due to instrumentation costs. Third generation sequencing platforms, such as Nanopore sequencers, aim at overcoming these obstacles but, unfortunately, are not designed for cell-free DNA analysis.Here we present a customized workflow to exploit low-coverage Nanopore sequencing for the detection of copy number variations from plasma of cancer patients. Whole genome molecular karyotypes of 6 lung cancer patients and 4 healthy subjects were successfully produced with as few as 2 million reads, and common lung-related copy number alterations were readily detected.This is the first successful use of Nanopore sequencing for copy number profiling from plasma DNA. In this context, Nanopore represents a reliable alternative to Illumina sequencing, with the advantages of minute instrumentation costs and extremely short analysis time.The availability of protocols for Nanopore-based cell-free DNA analysis will make this analysis finally accessible, exploiting the full potential of liquid biopsy both for research and clinical purposes.

【 授权许可】

CC BY