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

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.

The Role of ctDNA in Gastric Cancer

“…A study using a plasma-based, whole-genome NGS panel in 44 patients with any stage gastric ( n = 39) and oesophageal cancer ( n = 5) revealed a ctDNA detection rate of approximately 39%, with a VAF range of 2.5–8%. Interestingly, the concordance with tissue was only 54% [ 33 ]. Another study of 29 patients with any stage GC showed a ctDNA detection rate of 91.3% using a targeted NGS panel, with a VAF ranging from 2.8% to 87.1% and an average of 5.4 somatic variants detected per patient.…”

The Role of Cell-Free DNA in Cancer Treatment Decision Making

“…The relationship between post-operative detection of tumor-specific mutations in cfDNA analysis and residual disease, as well as tumor relapse, was also proven in the case of breast, lungand pancreatic cancer [ 25 , 78 , 210 ]. In advanced esophageal cancer, ctDNA is highly diagnostic but it is not appropriate for early diagnosis of esophageal cancer [ 41 ]. Among colon cancer patients with stage II disease who did not receive adjuvant chemotherapy, those who had persistent tumor-specific mutations detected in the liquid biopsy had a risk of residual tumor which was 18 times higher ( p < 0.001) compared to patients with undetectable tumor-specific mutations [ 201 ].…”

Circulating Tumor DNA in Gastric and Gastroesophageal Junction Cancer

“…The detection of copy number alterations (CNAs) from liquid biopsy would circumvent the need for surgical procedures in cases where not enough primary material is acquired or in the case of re-testings during the course of treatment. CNAs can reliably be detected from cfDNA [26] and were identified in gastric cancer for ERBB2 and FGFR2 by NGS [27,28] or digital droplet PCR (ddPCR) [29,30]. Thus, the profiling cfDNA can aid in identifying suitable treatment modalities for patients.…”