Trait: esophageal adenocarcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000478
Description A malignant tumor with glandular differentiation arising predominantly from Barrett mucosa in the lower third of the esophagus. Rare examples of esophageal adenocarcinoma deriving from ectopic gastric mucosa in the upper esophagus have also been reported. Grossly, esophageal adenocarcinomas are similar to esophageal squamous cell carcinomas. Microscopically, adenocarcinomas arising in the setting of Barrett esophagus are typically papillary and/or tubular. The prognosis is poor. [NCIT: C4025]
Trait categories
Cancer
Digestive system disorder
Synonyms 11 synonyms
  • EAC
  • adenocarcinoma - esophagus
  • adenocarcinoma - oesophagus
  • adenocarcinoma of esophagus
  • adenocarcinoma of oesophagus
  • adenocarcinoma of the esophagus
  • adenocarcinoma of the oesophagus
  • esophageal adenocarcinoma
  • esophagus adenocarcinoma
  • oesophageal adenocarcinoma
  • oesophagus adenocarcinoma
Mapped terms 12 mapped terms
  • DOID:4914
  • EFO:0000478
  • GARD:16927
  • ICD10:C15.2
  • ICD10:C15.5
  • MONDO:0005028
  • NCIT:C4025
  • OMIM:109350
  • ONCOTREE:ESCA
  • Orphanet:99976
  • SCTID:276803003
  • UMLS:C0279628

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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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
PGS003388
(best_ESCA_EA)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Esophageal adenocarcinoma esophageal adenocarcinoma 356,743
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003388/ScoringFiles/PGS003388.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 —
PPM016263 PGS003388
(best_ESCA_EA)
 PSS010077|
European Ancestry|
270,026 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: esophageal adenocarcinoma — AUROC: 0.814 R²: 0.00875 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