Genomic alterations in histologically clear low grade dysplasia resection margins forecast advanced neoplasia in ulcerative colitis

Background Endoscopic resection is used for the management of dysplasia in ulcerative colitis (UC), but a subset of patients develop subsequent advanced neoplasia (AN), i.e., high-grade dysplasia and/or colorectal cancer, despite apparently complete resection with histologically clear margins. Current risk stratification relies predominantly on histopathological and procedural features, which does not capture underlying genomic field cancerization of morphologically normal mucosa. Objective To determine whether genomic alterations within histologically non-dysplastic resection margins are associated with subsequent neoplastic progression following endoscopic resection of UC-associated dysplasia. Design We analysed a retrospective cohort of 51 UC patients, who underwent endoscopic resection of dysplastic lesions at a tertiary referral centre, with a median follow-up of 1947 days. 11 of these had local progression. We performed low-coverage whole genome sequencing (lcWGS) of 56 dysplastic lesions and 91 adjacent histologically non-dysplastic margins. Somatic copy number alteration (CNA) burden and phylogenetic analysis were correlated with progression to AN . Results Histologically non-dysplastic margins from lesions that subsequently progressed to AN demonstrated significantly higher CNA burden compared with non-progressors. In multivariate analysis high margin CNA burden was independently associated with local progression, whereas histologically clear resection margins and en bloc excisions were not. Conclusion Histological clearance does not necessarily indicate clearance of the cancerised field in UC-associated dysplasia. Genomic detection of field cancerisation within histologically non-dysplastic resection margins identifies patients at increased risk of subsequent neoplasia and provides a potential biomarker for biologically informed post-resection surveillance.