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 minimise 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 two out of four 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. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.