Abstract: Introduction: Copy number changes are important in the progression of Barrett’s esophagus to esophageal adenocarcinoma “EAC” (Li et al 2014). Shallow whole genome sequencing “sWGS” has been established as a cost effective method of investigating copy number changes in formalin fixed paraffin embedded “FFPE” tissue (Scheinin et al 2014). We aimed to optimise methodology in EAC and evaluate copy number changes in the evolution of Barrett’s. Methods: We compared 50X WGS on frozen tissue with 0.1X WGS from FFPE tumour material from the same patient. In order to address poor cellularity in Biopsies, sWGS data from a 50% cellularity biopsy with a 90% frozen sample from a single patient were compared. Accounting for poor biopsy cellularity 0.4X coverage was used. We performed FFPE sWGS on 895 samples from a 90 patient cohort: 1:1 ratio of patients who progressed to high grade dysplasia “HGD” and patients who never progressed. 3-31 samples per patient were collected over time and space throughout surveillance (median 4.5 and 7.3 years for progressor’s and non-progressor’s respectively). Data was processed using QDNAseq, Piece Wise Constant Fitting Segmenter and the coefficient of variation. Results: During optimisation, 97% of copy number changes were detected in both frozen and FFPE samples from spatially distinct tumour regions. A classical EAC profile was observed with oncogene amplifications and SMAD4 deletion. We found 91% and 93% agreement in copy number calls using orthogonal platforms between 90% and 50% cellularity samples from one tumour. Changes observed included amplifications in known cancer genes such as MECOM, EGFR and GATA4 and p16 and RUNX1 deletions. In Barrett’s we observed significantly larger changes (base pair length) in progressor’s compared with non-progressor’s (P=0.0017) and a trend towards higher numbers of chromosomal regions called as variable in progressor’s (mean 45.25 vs 9.25 in progressor’s and non-progressor’s respectively). Common to both cohorts was loss of tumour suppressor genes including p16 and FHIT while, unique to progressor’s, we identified oncogene amplifications such as CDK6 and ERBB3. Heterogeneity within lesions over time as well as at individual endoscopies highlights spatial heterogeneity within individ- ual lesions and, therefore, difficulties associated with sampling bias. Conclusions: sWGS has been optimised to detect copy number changes in EAC and Barrett’s. We have investigated copy number changes in over 800 samples from a large, well clinically annotated cohort. The patterns we observe include larger and more frequent copy number changes in patients progressing to HGD, high levels of heterogeneity between samples over time as well as within a lesion at a specific time point and increased oncogene amplifications in progressor patients.