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 35 synonyms
  • (ulcerative esophagitis) or (Barrett's esophagus)
  • BE
  • Barrett Epithelium
  • Barrett Esophagus
  • Barrett Syndrome
  • Barrett esophagus
  • Barrett esophagus/esophageal adenocarcinoma
  • Barrett metaplasia
  • Barrett's Syndrome
  • Barrett's esophagus
  • Barrett's esophagus (disorder)
  • Barrett's esophagus (disorder) [Ambiguous]
  • Barrett's esophagus with esophagitis
  • Barrett's esophagus with esophagitis (disorder)
  • Barrett's oesophagus
  • Barrett's oesophagus with esophagitis
  • Barrett's ulcer of esophagus
  • Barrett's ulcer of esophagus (disorder)
  • Barrett's ulcer of oesophagus
  • Barretts Esophagus
  • Barretts syndrome
  • CLE
  • Epithelium, Barrett
  • Esophagus, Barrett
  • Esophagus, Barrett's
  • Syndrome, Barrett
  • Syndrome, Barrett's
  • adenocarcinoma of esophagus
  • adenocarcinoma of oesophagus
  • cello
  • columnar epithelial-lined Lower esophagus
  • columnar epithelial-lined Lower oesophagus
  • columnar-lined esophagus
  • columnar-lined oesophagus
  • ulcerative esophagitis
Mapped terms 14 mapped terms
  • DOID:9206
  • ICD9:530.85
  • MEDGEN:2551
  • MESH:D001471
  • MONDO:0013662
  • MeSH:D001471
  • MedDRA:10004134
  • NCIT:C2891
  • NCIt:C2891
  • OMIM:614266
  • Orphanet:1232
  • SCTID:196609006
  • SNOMEDCT:302914006
  • UMLS:C0004763

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Ancestry legend
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003387
(best_ESCA_BEEA)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Esophageal adenocarcinoma or Barrett’s esophagus Barrett's esophagus,
esophageal adenocarcinoma		 601,980
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003387/ScoringFiles/PGS003387.txt.gz

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) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM016262 PGS003387
(best_ESCA_BEEA)
 PSS010077|
European Ancestry|
270,026 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: esophageal adenocarcinoma — AUROC: 0.819 R²: 0.0123 age, sex, top 20 genetic principal components —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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
PSS010077 C15, histology was one of the followings: Adenocarcinoma, NOS; Adenocarcinoma, intestinal type; Adenocarcinoma in tubulovillous adenoma —
[
  • 482 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer