Shallow Whole Genome Sequencing can detect Copy Number Changes in FFPE material from Oesophageal Adenocarcinoma and Barrett’s Oesophagus


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Eleanor Gregson1,David Wedge2,Matthew Eldridge3,Lawrence Bower3,Ahmad Miremadi4,Rebecca Fitzgerald5
1MRC Cancer Unit, University of Cambridge,2Big Data Institute, University of Oxford,3Cancer Research UK Cambridge Institute, University of Cambridge,,4Cambridge University Hospitals NHS Foundation Trust,5MRC Cancer Cell Unit, University of Cambridge



Copy number (CN) changes are important in the progression of Barrett’s Oesophagus to oesophageal adenocarcinoma (OAC). Shallow whole genome sequencing (sWGS) has been established as a cost effective method of investigating CN changes in formalin fixed paraffin embedded (FFPE) tissue. We aimed to evaluate this methodology in the evolution of OAC.


We compared 50X WGS on frozen tissue with 0.1X WGS from FFPE material from the same patient. We performed FFPE sWGS on 5 Barrett’s patients who progressed to high grade dysplasia and 5 who never progressed. 3-25 samples per patient were collected over time and space throughout surveillance (median 8 years).  Accounting for poorer biopsy cellularity 0.4X coverage was used. Data was processed using QDNAseq, Piece Wise Constant Fitting Segmenter and the coefficient of variation.


During optimisation, 97% of CN changes were detected in both frozen and FFPE samples from spatially distinct tumour regions. A classical OAC profile was observed with oncogene amplifications and SMAD4 deletion.

We found 91% agreement in copy number calls between 90% and 20% cellularity FFPE samples from one tumour. Changes observed included amplifications in MECOM, EGFR and GATA4 and p16 and RUNX1 deletions.

In Barrett’s we observed larger changes in progressor’s compared with non-progressor’s (mean 6.6Mb vs 2.5Mb respectively, P=0.044). Loci specific changes in Barrett’s included p16 and FHIT loss in both cohorts and, as expected, a trend towards higher numbers of variable regions in progressor’s. Unique to progressor’s we identified oncogenes amplifications such as MECOM, EGFR and MYC as well as RUNX1 and SMAD4 loss. Heterogeneity within lesions over time as well as at individual endoscopies highlighted spatial heterogeneity.


sWGS can identify CN changes in OAC and Barrett’s. We plan to use this technology in a larger cohort of Barrett’s patients to better understand drivers of carcinogenesis.