Characterisation of dysplastic liver nodules using low-pass sequencing and the proof of principle on liquid biopsies

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 arm-level somatic copy number alterations (SCNAs) that characterise the transition of liver nodules through the cirrhosis-dysplasia-carcinoma axis. Subsequently, as a proof of principle, we validated our findings on an independent cohort using liquid biopsies. A repository of non-cancer DNA obtained from patients with HCC (n=389) was used to generate cut-off thresholds aiming to minimize false positive SCNAs. Samples representing stages from the multistep process of hepatocarcinogenesis (n=184) were sequenced by low-pass whole genome sequencing. 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 OR 35.5 (95% CI 11.5-110) and 16 (95% CI 6.4-40.2) respectively (p<0.0001). In an independent cohort (n=22), at least 2 out of the 4 alterations (1q+, 4q-, 8p- and 8q+) were detectable using liquid biopsies in all patients with HCC. Arm-level SCNAs on 1q+ or 8q+ are associated with high-risk liver pathology. These can be detected on liquid biopsy using low-pass sequencing which may be a future early cancer screening tool for patients with liver cirrhosis.