Molecular CancerCancer BiologyPeer-reviewed journal article
Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients
F. Martignano, S. Crucitta, A. Mingrino, R. Semeraro, M. Del Re, I. Petrini, A. Magi, S. G. Conticello
Abstract
Alterations in the genetic content, such as Copy Number Variations (CNVs) is one of the hallmarks of cancer and their detection is used to recognize tumoral DNA. Analysis of cell-free DNA from plasma is a powerful tool for non-invasive disease monitoring in cancer patients. Here we exploit third generation sequencing (Nanopore) to obtain a CNVs profile of tumoral DNA from plasma, where cancer-related chromosomal alterations are readily identifiable. Compared to Illumina sequencing -the only available alternative- Nanopore sequencing represents a viable approach to characterize the molecular phenotype, both for its ease of use, costs and rapid turnaround (6 hours).
- organism: human
- assay: whole-genome sequencing
- research focus: variant calling
- research focus: differential expression
- approach: deep learning
- approach: statistical model
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
Li‐Ting Chen, Myrthe Jager, … Jeroen de Ridder·Genome ResearchPeer-reviewed·Apr 1, 2025
- Profiling copy number alterations in cell-free tumour DNA using a single-reference
Alan J. Robertson, Qinying Xu, … Lachlan Coin·bioRxiv·Mar 28, 2018
- High resolution copy number inference in cancer using short-molecule nanopore sequencing
Timour Baslan, Sam Kovaka, … Michael C. Schatz·Nucleic Acids ResearchPeer-reviewed·Sep 9, 2021
- Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
Billy T. Lau, Alison Figueroa Almeda, … Hanlee P. Ji·Genome MedicinePeer-reviewed·May 3, 2023
- Accurate detection of circulating tumor DNA using nanopore consensus sequencing
A. Marcozzi, M. Jager, … J. de Ridder·bioRxiv·Jul 14, 2020
- LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations
Eszter Lakatos, Helen Hockings, … Trevor A. Graham·iSciencePeer-reviewed·Jul 21, 2021