Characterisation of dysplastic liver nodules using low-pass DNA sequencing and detection of chromosome arm-level abnormalities in blood-derived cell-free DNA

Abstract

High grade dysplasia carries significant risk of transformation to hepatocellular carcinoma (HCC). Despite this, at the current standard of care, all non-malignant hepatic nodules including high grade dysplastic nodules are managed similarly. This is partly related to difficulties in distinguishing high-risk pathology in the liver. We aimed to identify chromosome arm-level somatic copy number alterations (SCNAs) that characterise the transition of liver nodules along the cirrhosis-dysplasia-carcinoma axis. We validated our findings on an independent cohort using blood-derived cell-free DNA. A repository of non-cancer DNA sequences obtained from patients with HCC (n=389) was analysed to generate cut-off thresholds aiming to minimize false positive SCNAs. Tissue samples representing stages from the multistep process of hepatocarcinogenesis (n=184) were subjected to low-pass whole genome sequencing. Chromosome arm-level SCNAs were identified in liver cirrhosis, dysplastic nodules, and HCC to assess their discriminative capacity. Samples positive for 1q+ or 8q+ arm-level duplications were likely to be either HCC or high-grade dysplastic nodules as opposed to low grade dysplastic nodules or cirrhotic tissue with an Odds Ratio (OR) of 35.5 (95% CI 11.5-110) and 16 (95% CI 6.4-40.2) respectively (p<0.0001). In an independent cohort of patients recruited from Nottingham, UK, at least 2 out of 4 alterations (1q+, 4q-, 8p- and 8q+) were detectable in blood-derived cell-free DNA of patients with HCC (n=22) but none of the control patients with liver cirrhosis (n=9). Arm-level SCNAs on 1q+ or 8q+ are associated with high-risk liver pathology. These can be detected using low-pass sequencing of cell-free DNA isolated from blood which may be a future early cancer screening tool for patients with liver cirrhosis. This article is protected by copyright. All rights reserved.