Alvin Ng from the Early Cancer Institute at the University of Cambridge in the UK presented at London Calling 2022 on “Early detection of Barrett’s esophagus and esophageal adenocarcinoma using Oxford Nanopore long-read sequencing.” They began by explaining Barrett’s esophagus (BE) as the pre-malignant condition of esophageal adenocarcinoma (EAC) and has three stages: non-dysplastic, low-grade dysplastic, and high-grade dysplastic. EAC has low survival: 50%. Molecular alterations increase and accumulate in the development of EAC. Ng noted that copy number changes are a predominant feature in patients that progress to disease. they also indicated that complex rearrangements are “frequent & alter driver genes.” Ng and team had the goal of using Oxford Nanopore Technologies (ONT) as an “all-in one” detection system. They used an sv workflow. They used a PromethION flow cell for sequencing. Their results indicated a variety of alternations and copy number changes. They detected deletions in 7/9 and 5/9 BE tissues sequenced. There was a higher copy number in the tumor. Ng concluded that the detection of FHIT and CDKN2A loss in BE could be used for diagnosis. These events seem to be early in the process. Ng shared data from de novo assemblies of complex sequence variants. Several alterations could be detected and applied for the early detection of BE and EAC.
