Fig. 1. Study design and sequencing strategy.

a Examples of representative cases selected for sequencing, with surveillance endoscopies over time and the highest grade at the time point detailed: indolent non-dysplastic; cases which progressed to low-grade dysplasia (LGD) high-grade dysplasia (HGD) or intramucosal carcinoma (IMC); cases sampled prior to progression to dysplasia; Barrett’s esophagus (BE) sampled from adjacent to esophageal adenocarcinoma, at the cancer time point. The highest available pathology grade frozen biopsy was used for sequencing. Examples of frozen biopsy histology are shown. Gender, median follow-ups after the sequenced sample and median age and range detailed. b Flow diagram detailing cohort creation. 149 high-cellularity, triple pathology reviewed, single-time point BE biopsies sequenced from 149 individual patients with different disease trajectories were sequenced. c For each patient, one biopsy underwent whole-genome sequencing (WGS) at 50×, whole-transcriptome sequencing and methylation with the EPIC 850k array, where sufficient material was available. Three samples were later excluded due to genomic mismatch or poor coverage, resulting in an analysed cohort of 146 patients. The Venn diagram shows the numbers of biopsies sequenced with each modality.