title: DNA methylation as an adjunct to histopathology to detect prevalent, inconspicuous dysplasia and early-stage neoplasia in Barrett's esophagus.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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).
  
  
  CONCLUSIONS
  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.
authors.affiliation: MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, UK.
authors.forename: Muhammad A
authors.initials: MA
authors.lastname: Alvi
authors.forename: Xinxue
authors.initials: X
authors.lastname: Liu
authors.forename: Maria
authors.initials: M
authors.lastname: O'Donovan
authors.forename: Richard
authors.initials: R
authors.lastname: Newton
authors.forename: Lorenz
authors.initials: L
authors.lastname: Wernisch
authors.forename: Nicholas B
authors.initials: NB
authors.lastname: Shannon
authors.forename: Kareem
authors.initials: K
authors.lastname: Shariff
authors.forename: Massimiliano
authors.initials: M
authors.lastname: di Pietro
authors.forename: Jacques J G H M
authors.initials: JJ
authors.lastname: Bergman
authors.forename: Krish
authors.initials: K
authors.lastname: Ragunath
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Fitzgerald
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D001471:Barrett Esophagus / Q000235:genetics* / Q000473:pathology; D019175:DNA Methylation / Q000235:genetics*; D050172:Genes, X-Linked; D018392:Genomic Imprinting; D006801:Humans; D009367:Neoplasm Staging; D009369:Neoplasms / Q000235:genetics / Q000473:pathology; D012307:Risk Factors