Trait: Barrett's esophagus

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000280
Description Esophageal lesion lined with columnar metaplastic epithelium which is flat or villiform. Barrett epithelium is characterized by two different types of cells: goblet cells and columnar cells. The symptomatology of Barrett esophagus is that of gastro-esophageal reflux. It is the precursor of most esophageal adenocarcinomas. (WHO) [NCIT: C2891]
Trait category
Digestive system disorder
Synonyms 27 synonyms
  • Barrett's ulcer of esophagus
  • BE
  • Barrett esophagus
  • columnar-lined esophagus
  • (ulcerative esophagitis) or (Barrett's esophagus)
  • Esophagus, Barrett
  • Barrett's esophagus (disorder)
  • Barrett's esophagus with esophagitis (disorder)
  • Barretts Esophagus
  • Barrett's esophagus
  • Barrett Esophagus
  • Barrett's esophagus (disorder) [Ambiguous]
  • Syndrome, Barrett's
  • Barrett's ulcer of esophagus (disorder)
  • Barrett's esophagus with esophagitis
  • Barrett Syndrome
  • Syndrome, Barrett
  • cello
  • Barretts syndrome
  • columnar epithelial-lined Lower esophagus
  • Epithelium, Barrett
  • Esophagus, Barrett's
  • Barrett's oesophagus
  • ulcerative esophagitis
  • Barrett's Syndrome
  • CLE
  • Barrett Epithelium
Mapped term(s) 13 mapped terms
  • SCTID:196609006
  • MONDO:0013662
  • MSH:D001471
  • MESH:D001471
  • NCIT:C2891
  • SNOMEDCT:302914006
  • ICD10:K22.7
  • OMIM:614266
  • DOID:9206
  • NCIt:C2891
  • ICD9:530.85
  • ICD10:K22.70
  • COHD:443344

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000085 CC_Stomach PGP000050 Graff RE et al. bioRxiv (2020) Pre Esophageal and stomach cancers gastric carcinoma
Barrett's esophagus
13 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000085/ScoringFiles/PGS000085.txt.gz

PGS Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID
(PPM ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000205 PGS000085 (CC_Stomach) PSS000124 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Esophageal and stomach cancers OR: 1.07[1.0, 1.13] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000124 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21010 and 21020
[
  • 1,094 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB