Trait: esophageal cancer

Trait Information
Identifier MONDO_0007576
Description A primary or metastatic malignant neoplasm involving the esophagus. [NCIT: C7478]
Trait categories
Cancer
Digestive system disorder
Synonyms 49 synonyms
  • Aerodigestive tract cancer, susceptibility to
  • Ca lower third esophagus
  • Ca lower third oesophagus
  • Ca middle third esophagus
  • Ca middle third oesophagus
  • Escc, susceptibility to
  • cancer of esophagus
  • cancer of oesophagus
  • esophageal cancer
  • esophageal cancer, somatic
  • esophageal carcinoma, somatic
  • esophageal squamous cell carcinoma, somatic
  • esophageal squamous cell carcinoma, susceptibility to
  • esophagus cancer
  • gastric cardia adenocarcinoma, susceptibility to
  • malignant esophageal neoplasm
  • malignant esophageal tumor
  • malignant esophageal tumour
  • malignant esophagus neoplasm
  • malignant esophagus tumor
  • malignant neoplasm of distal third of esophagus
  • malignant neoplasm of distal third of oesophagus
  • malignant neoplasm of esophagus
  • malignant neoplasm of lower third of esophagus
  • malignant neoplasm of lower third of oesophagus
  • malignant neoplasm of middle third of esophagus
  • malignant neoplasm of middle third of oesophagus
  • malignant neoplasm of oesophagus
  • malignant neoplasm of proximal third of esophagus
  • malignant neoplasm of proximal third of oesophagus
  • malignant neoplasm of the esophagus
  • malignant neoplasm of the oesophagus
  • malignant neoplasm of upper third esophagus
  • malignant neoplasm of upper third oesophagus
  • malignant oesophagus neoplasm
  • malignant oesophagus tumour
  • malignant tumor of abdominal esophagus
  • malignant tumor of distal third of esophagus
  • malignant tumor of esophagus
  • malignant tumor of proximal third of esophagus
  • malignant tumor of the esophagus
  • malignant tumor of the middle third of the esophagus
  • malignant tumour of abdominal oesophagus
  • malignant tumour of distal third of oesophagus
  • malignant tumour of oesophagus
  • malignant tumour of proximal third of oesophagus
  • malignant tumour of the middle third of the oesophagus
  • malignant tumour of the oesophagus
  • oesophagus cancer
Mapped terms 14 mapped terms
  • DOID:5041
  • ICD9:150.2
  • ICD9:150.3
  • ICD9:150.4
  • ICD9:150.5
  • ICD9:150.8
  • ICD9:150.9
  • NCIT:C4764
  • NCIT:C7478
  • OMIM:133239
  • SCTID:187724003
  • SCTID:363402007
  • UMLS:C0496775
  • UMLS:C0546837
Child trait(s) 2 child traits

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:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows all PGS for "esophageal cancer" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000363
(PRSWEB_PHECODE150_C15_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Cancer of esophagus esophageal cancer 1,081,646
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000363/ScoringFiles/PGS000363.txt.gz
PGS000364
(PRSWEB_PHECODE150_C15_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Cancer of esophagus esophageal cancer 2,001
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000364/ScoringFiles/PGS000364.txt.gz
PGS000365
(PRSWEB_PHECODE150_C3-OESOPHAGUS_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Cancer of esophagus esophageal cancer 1,070,434
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000365/ScoringFiles/PGS000365.txt.gz
PGS000366
(PRSWEB_PHECODE150_UKBB-SAIGE-HRC-X150_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Cancer of esophagus esophageal cancer 1,119,238
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000366/ScoringFiles/PGS000366.txt.gz
PGS002298
(PRS14_esophageal)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Esophageal cancer esophageal carcinoma 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002298/ScoringFiles/PGS002298.txt.gz
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
PPM001048 PGS000363
(PRSWEB_PHECODE150_C15_PRS-CS_MGI_20200608)
 PSS000537|
European Ancestry|
2,064 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of esophagus OR: 1.249 [1.075, 1.45]
β: 0.222 (0.0762)		 AUROC: 0.564 [0.525, 0.604] Nagelkerke's Pseudo-R²: 0.0089
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 2.84 [1.07, 7.54]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE150_C15_PRS-CS_MGI_20200608
PPM001049 PGS000364
(PRSWEB_PHECODE150_C15_LASSOSUM_MGI_20200608)
 PSS000537|
European Ancestry|
2,064 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of esophagus OR: 1.203 [1.041, 1.391]
β: 0.185 (0.074)		 AUROC: 0.551 [0.51, 0.588] Nagelkerke's Pseudo-R²: 0.00648
Brier score: 0.0826
Odds Ratio (OR, top 1% vs. Rest): 1.81 [0.56, 5.82]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE150_C15_LASSOSUM_MGI_20200608
PPM001050 PGS000365
(PRSWEB_PHECODE150_C3-OESOPHAGUS_PRS-CS_MGI_20200608)
 PSS000537|
European Ancestry|
2,064 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of esophagus OR: 1.187 [1.021, 1.38]
β: 0.171 (0.0769)		 AUROC: 0.553 [0.514, 0.596] Nagelkerke's Pseudo-R²: 0.00521
Brier score: 0.0826
Odds Ratio (OR, top 1% vs. Rest): 1.27 [0.329, 4.9]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE150_C3-OESOPHAGUS_PRS-CS_MGI_20200608
PPM001051 PGS000366
(PRSWEB_PHECODE150_UKBB-SAIGE-HRC-X150_PRS-CS_MGI_20200608)
 PSS000537|
European Ancestry|
2,064 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of esophagus OR: 1.24 [1.067, 1.441]
β: 0.215 (0.0766)		 AUROC: 0.564 [0.522, 0.605] Nagelkerke's Pseudo-R²: 0.00839
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 1.28 [0.332, 4.95]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE150_UKBB-SAIGE-HRC-X150_PRS-CS_MGI_20200608
PPM013027 PGS002298
(PRS14_esophageal)
 PSS009661|
European Ancestry|
406 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Esophageal cancer — AUROC: 0.53 [0.51, 0.56] — — —
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
PSS009661 esophageal cancer (ICD-9 = 150 or ICD-10 = C15) — 406 individuals — European — UKB —
PSS000537 PheCode:150; ICD9CM:150.0, 150.1, 150.2, 150.3, 150.4, 150.5, 150.8, 150.9, 230.1, V10.03; ICD10CM:C15, C15.3, C15.4, C15.5, C15.8, C15.9, D00.1 —
[
  • 188 cases
  • , 1,876 controls
]
 — European — MGI —