Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Using DNA methylation to detect dysplasia/early neoplasia in Barrett's carcinogenesis

ABSTRACT: Dysplasia and early cancer are hard to detect in endoscopic biopsies and hence this study was carried out to evaluate the biomarker potential of DNA methylation to detect dyspasia and early cancer in Barrett's esophaghus patients. Bisulfite converted genomic DNA was hybridized onto Illumina 27k methylation arrays.

ORGANISM(S): Homo sapiens

PROVIDER: GSE32925 | GEO | 2013/01/28

SECONDARY ACCESSION(S): PRJNA146489

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Using DNA methylation to detect dysplasia/early neoplasia in Barrett's carcinogenesis

Project description:Dysplasia and early cancer are hard to detect in endoscopic biopsies and hence this study was carried out to evaluate the biomarker potential of DNA methylation to detect dyspasia and early cancer in Barrett's esophaghus patients. Bisulfite converted genomic DNA was hybridized onto Illumina 27k methylation arrays. 22 Barrett's esophagus (BE) and 2 Duodenum vs. 24 esophageal adenocarcinoma (EAC)

2013-01-28 | E-GEOD-32925 | biostudies-arrayexpress

Gene expression profile in Barrett's esopahgus

Project description:Microarray was used to identify differential gene expression pattern in Barrett's esophagus (BE), compared to the normal adjacent epithelia gastric cardia (GC) and normal squamous esophagus (NE) RNA was extraxted from endoscopic biopsies of BE (n=10), GC (n=10) and NE (n=10, only 8 uploaded). One NE sample was excluded since clustered with BE and all the intestinal markers were positive, indicating sampling error.

2012-03-29 | E-GEOD-34619 | biostudies-arrayexpress

Transformation of Dysplasia in Barrett's Esophagus

Project description:Transformation of Dysplasia in Barrett's Esophagus

| PRJNA782730 | ENA

Transformation of Dysplasia in Barrett's Esophagus

Project description:Transformation of Dysplasia in Barrett's Esophagus

| PRJNA782731 | ENA

Barrett's esophagus

2006-06-28 | GSE5155 | GEO

Barrett's esophagus

Project description:Barrett's esophagus transcriptome was analysed and compared with Barrett's esophagus primary cell culture and esophageal adenocarcinoma. Keywords: SAGE analysis to compare tissues Barrett's esophagus biopsy was taken from 1 male metaplastic Barrett's esophagus patient. Barrett's esophagus primary cell culture was cultures from a biopsy taken from a Barrett's esophagus patient and cultured for about 4 to 5 weeks. Esophageal adenocarcinoma was taken from a patient known to have cancer and previously Barrett's esophagus

2006-06-28 | E-GEOD-5155 | biostudies-arrayexpress

DNA methylation as an adjunct to histopathology to detect prevalent, inconspicuous dysplasia and early-stage neoplasia in Barrett's esophagus.

Project description:PURPOSE:Endoscopic surveillance of Barrett's esophagus is problematic because dysplasia/early-stage neoplasia is frequently invisible and likely to be missed because of sampling bias. Molecular abnormalities may be more diffuse than dysplasia. The aim was therefore to test whether DNA methylation, especially on imprinted and X-chromosome genes, is able to detect dysplasia/early-stage neoplasia. EXPERIMENTAL DESIGN:27K methylation arrays were used to find genes best able to differentiate between 22 Barrett's esophagus and 24 esophageal adenocarcinoma (EAC) samples. These were validated using pyrosequencing on a retrospective cohort (60 Barrett's esophagus, 36 dysplastic, and 90 EAC) and then in a prospective multicenter study (98 Barrett's esophagus patients, including 28 dysplastic and 9 early EAC) designed to utilize biomarkers to stratify patients according to their prevalent dysplasia/EAC status. RESULTS:Genes (23%) on the array, including 7% of X-linked and 69% of imprinted genes, have shown statistically significant changes in methylation in EAC versus Barrett's esophagus (Wilcoxon P < 0.05). 6/7 selected candidate genes were successfully internally (Pearson's P < 0.01) and externally validated (ANOVA P < 0.001). Four genes (SLC22A18, PIGR, GJA12, and RIN2) showed the greatest area under curve (0.988) to distinguish between Barrett's esophagus and dysplasia/EAC in the retrospective cohort. This methylation panel was able to stratify patients from the prospective cohort into three risk groups based on the number of genes methylated (low risk: <2 genes, intermediate: 2, and high: >2). CONCLUSION:Widespread DNA methylation changes were observed in Barrett's carcinogenesis including ?70% of known imprinted genes. A four-gene methylation panel stratified patients with Barrett's esophagus into three risk groups with potential clinical utility.

| S-EPMC4998953 | biostudies-literature

Oncoscan SNP-array analysis of DNA from esophageal samples of patients with Barrett's esophagus before and after progression to esophageal dysplasia and adenocarcinoma

Project description:The goal of this experiment is to characterize the copy number changes in esophageal mucosa of patients with Barrett's esophagus (BE) who progress to esophageal dysplasia and adenocarcinoma (BE progressors), as compared to patients with BE who do not progress for at least two years after esophageal mucosal sampling (non-progressors with never dysplastic Barrett's esophagus - NvDBE - samples). We sampled esophageal mucosa from the following groups: 1) non-dysplastic intestinal metaplasia from 16 patients at least 1 year before progression to esophageal dysplasia or adenocarcinoma (PP-BE); 2) non-dysplastic intestinal metaplasia from 21 patients who did not progress to dysplasia or adenocarcinoma for at least 2 years of surveillance after the tested sample (NvDBE) 3) non-dysplastic intestinal metaplasia from 21 patients who had temporally concurrent but spatially separate intestinal metaplasia samples from the same procedure (C-BE). 4) 10 samples of esophageal dysplasia or adenocarcinoma from patients in group 1 and 3. Samples were obtained by endoscopic biopsy, endomucosal resection or surgical resection, processed for clinical purposes by routine histopathologic methods, including formalin fixation and paraffin embedding (FFPE). DNA was extracted from 5 micro tissue sections of FFPE blocks and DNA extracted using QIAamp DNA FFPE Tissue Kit (Qiagen, Germantown, MD). Samples were processed for identification of somatic copy number alterations using the OncoScan FFPE Assay or the OncoScan CNV Assay (Affymetrix, Santa Clara, CA) according to the manufacturer's protocols. After hybridization, the arrays were washed, stained using GeneChip Fluidics Station 450 (Affymetrix) and scanned using GeneChip Scanner 3000 7G (Affymetrix). The CEL files generated are deposited here.

2019-10-27 | E-MTAB-7396 | biostudies-arrayexpress

The microRNA profile in neosquamous oesophageal mucosa following ablation of Barrett's oesophagus

Project description:mucosal biopsies were taken from patients at pre and post-argon plasma coagulation (APC) ablation of Barrett's oesophagus, and from healthy controls. Total RNA was extracted using Trizol. miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a high throughput TaqMan® OpenArray® Human microRNA panel (Life technologies, #4461104). The panel consisted of probes for 754 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v14. Endoscopic surveillance remains the mainstay of cancer prevention in individuals with Barrett’s oesophagus, and definitive management by surgery or endoscopy is reserved for high grade dysplasia or cancer. There are several endoscopic treatments that are widely used for Barrett’s oesophagus, including argon plasma coagulation (APC). The normality of the regenerated neosquamous epithelium after ablation has been called into question. In the current study we profiled global microRNA expression in oesophageal mucosa before and after ablation of Barrett’s oesophagus using Argon plasma coagulation. Our aim was to investigate differences in microRNA expression between neosquamous and normal squamous tissues.

2017-09-14 | GSE94854 | GEO

microRNA/UCR expression profiling of human Barrett's carcinogenesis

Project description:To test the hypothesis that there are specific miRNA/UCR expression signature which characterizes Barrett's esophagus development and progression, we performed miRNA/UCR microarray analysis comparing normal esophageal squamous epithelium with all the phenotypic lesions seen in the Barrett's carcinogenic process

2010-01-30 | GSE20099 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data