Genome-wide methylation analysis reveals methylation subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma

Methylation-based subtypes were identified in nondysplastic Barrett's Esophagus (BE) from BE-only patients (n=62) and Esophageal Adenocarcinoma (n=23) using RPMM-based clustering on methylation data at probes with the most variant Beta-values on the HM450 platform. Samples in these methylation-based subtypes were further identified in the TCGA EAC dataset, and subtypes were characterized using integrated analysis of methylation, sequencing, and expression data. Bisulphite-converted DNA from 89 samples (n=23 EAC; n=62 BE from BE-only patients; n=7 BE from EAC patients) was processed using the HM450 platform. In the EAC subset, the 1515 Infinium probes with most variant Beta-value methylation were used in RPMM clustering to identify methylation-based subtypes. Methylation at these MVPs and RPMM-clustering was also used to identify subtypes in the subset of BE samples from BE patients. Methylation-based subtypes in EAC were further identified in EAC samples from the Cancer Genome Atlas and the cohort published by Krause et al 2016 (GSE72872), the molecular characteristics of the subtypes in EAC and BE were assessed using sequence and expression data, and a six-CpG probe panel was designed to identify HM and non-HM samples.