Molecular characterization of Barrett’s esophagus at single cell resolution

Study ID Alternative Stable ID Type
EGAS00001005221 Other

Study Description

Backgrounds & Aims: Patient with Barrett’s esophagus (BE) have an increased risk to develop esophageal adenocarcinoma and are under periodical endoscopic surveillance for malignant transformation. Pathologists distinguish between different BE stages to identify high-risk patients, but this process remains difficult as stage-specific markers are still missing. We established BE organoid cultures, applied single cell sequencing approaches to identify differences in gene expression and genomic alterations, and validated candidate genes for their predictive value on histological sections. Methods: We collected 43 epithelial biopsies from 21 patients, established organoids for the clonal expansion of matching healthy and diseased tissue from two patients to identify genomic alterations by whole genome sequencing (WGS). We performed single cell DNA-sequencing (scDNAseq) to analyse DNA alterations within biopsies from 8 patients and single cell RNA-sequencing (scRNAseq) to identify gene expression differences between BE stages from 19 patients. Candidate marker genes were then ... (Show More)

Study Datasets 3 datasets.

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Dataset ID Description Technology Samples
14 samples were processed for single cell DNA sequencing
NextSeq 500 14
13 samples were processed by whole genome sequencing
Illumina NovaSeq 6000 13
17 samples were processed for single cell RNA sequencing (SORT-seq)
NextSeq 500 17

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