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Genomic copy number predicts oesophageal cancer years before transformation

By Sarah Killcoyne, Eleanor Gregson, David C Wedge, Dan J. Woodcock, Matthew Eldridge, Rachel de la Rue, Ahmad Miremadi, Sujath Abbas, Adrienn Blasko, Wladyslaw Januszewicz, Aikaterini Varanou Jenkins, Moritz Gerstung, Rebecca C. Fitzgerald

Posted 28 Feb 2020
bioRxiv DOI: 10.1101/2020.02.27.967612

Cancer arises through a process of somatic evolution and recent studies have shown that aneuploidies and driver gene mutations precede cancer diagnosis by several years to decades (1-4). Here, we address the question whether such genomic signals can be used for early detection and pre-emptive cancer treatment. To this end we study Barrett's oesophagus, a genomic copy number driven neoplastic precursor lesion to esophageal adenocarcinoma (5). We use shallow whole genome sequencing of 777 biopsies sampled from 88 patients in surveillance for Barrett's esophagus over a period of up to 15 years. These data show that genomic signals exist that distinguish progressive from stable disease with an AUC of 0.87 and a sensitivity of 50% even ten years prior to histopathological disease transformation. These finding are validated on two independent cohorts of 75 and 248 patients. Compared against current patient management guidelines genomic risk classification enables earlier treatment for high risk patients as well as reduction of unnecessary treatment and monitoring for patients who are unlikely to develop cancer.

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