Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients

PLoS One. 2021 Feb 4;16(2):e0245488. doi: 10.1371/journal.pone.0245488. eCollection 2021.

Abstract

Background: Analysis of cell-free tumour DNA, a liquid biopsy, is a promising biomarker for cancer. We have performed a proof-of principle study to test the applicability in the clinical setting, analysing copy number alterations (CNAs) in plasma and tumour tissue from 44 patients with gastro-oesophageal cancer.

Methods: DNA was isolated from blood plasma and a tissue sample from each patient. Array-CGH was applied to the tissue DNA. The cell-free plasma DNA was sequenced by low-coverage whole-genome sequencing using a clinical pipeline for non-invasive prenatal testing. WISECONDOR and ichorCNA, two bioinformatic tools, were used to process the output data and were compared to each other.

Results: Cancer-associated CNAs could be seen in 59% (26/44) of the tissue biopsies. In the plasma samples, a targeted approach analysing 61 regions of special interest in gastro-oesophageal cancer detected cancer-associated CNAs with a z-score >5 in 11 patients. Broadening the analysis to a whole-genome view, 17/44 patients (39%) had cancer-associated CNAs using WISECONDOR and 13 (30%) using ichorCNA. Of the 26 patients with tissue-verified cancer-associated CNAs, 14 (54%) had corresponding CNAs in plasma. Potentially clinically actionable amplifications overlapping the genes VEGFA, EGFR and FGFR2 were detected in the plasma from three patients.

Conclusions: We conclude that low-coverage whole-genome sequencing without prior knowledge of the tumour alterations could become a useful tool for cell-free tumour DNA analysis of total CNAs in plasma from patients with gastro-oesophageal cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenocarcinoma / blood*
  • Adenocarcinoma / epidemiology
  • Adenocarcinoma / genetics*
  • Adenocarcinoma / pathology
  • Adult
  • Aged
  • Aged, 80 and over
  • Biomarkers, Tumor / genetics
  • Biomarkers, Tumor / isolation & purification
  • Circulating Tumor DNA / genetics*
  • Circulating Tumor DNA / isolation & purification
  • DNA Copy Number Variations*
  • Esophageal Neoplasms / blood*
  • Esophageal Neoplasms / epidemiology
  • Esophageal Neoplasms / genetics*
  • Esophageal Neoplasms / pathology
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Liquid Biopsy
  • Male
  • Middle Aged
  • Pilot Projects
  • Stomach Neoplasms / blood*
  • Stomach Neoplasms / epidemiology
  • Stomach Neoplasms / genetics*
  • Stomach Neoplasms / pathology
  • Sweden / epidemiology
  • Whole Genome Sequencing

Substances

  • Biomarkers, Tumor
  • Circulating Tumor DNA

Grants and funding

KW, ET and MN are supported by grants from Region Stockholm (combined clinical residency and PhD training program: K2891-2016 and ALF-project: grant number 581046). CA17118 (European Cooperation in Science and Technology, www.cost.eu) has provided networking support to ET.