Trait: neoplasm of esophagus

Trait Information
Identifier MONDO_0021355
Description A neoplasm (disease) that involves the esophagus. [MONDO: patterns/location]
Trait category
Other trait
Synonyms 19 synonyms
  • esophageal neoplasm
  • esophageal neoplasms, benign and malignant
  • esophageal tumor
  • esophageal tumors
  • esophageal tumour
  • esophageal tumours
  • esophagus neoplasm
  • esophagus neoplasm (disease)
  • esophagus tumor
  • neoplasm of esophagus
  • neoplasm of the esophagus
  • neoplasm of the oesophagus
  • oesophagus neoplasm
  • oesophagus neoplasm (disease)
  • oesophagus tumour
  • tumor of esophagus
  • tumor of the esophagus
  • tumour of oesophagus
  • tumour of the oesophagus
Child trait(s) 3 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 PGS for child terms of "neoplasm of esophagus" in the EFO hierarchy.
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)
PGS000363
(PRSWEB_PHECODE150_C15_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Esophageal cancer 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)
 Esophageal cancer 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)
 Esophageal cancer 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)
 Esophageal cancer 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 carcinoma of esophagus 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 esophageal adenocarcinoma,
Barrett esophagus		 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
PGS005160
(PRS-ESC)
 PGP000711 |
Zhu M et al. PLoS Med (2025)
 Esophageal cancer carcinoma of esophagus 11
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005160/ScoringFiles/PGS005160.txt.gz
PGS018475
(TPMI_150_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Esophageal cancer esophageal cancer 5
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018475/ScoringFiles/PGS018475.txt.gz
PGS018476
(TPMI_150_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Esophageal cancer esophageal cancer 255,880
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018476/ScoringFiles/PGS018476.txt.gz
PGS018477
(TPMI_150_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Esophageal cancer esophageal cancer 30,188
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018477/ScoringFiles/PGS018477.txt.gz
PGS018478
(TPMI_150_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Esophageal cancer esophageal cancer 983,792
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018478/ScoringFiles/PGS018478.txt.gz
PGS018479
(TPMI_150_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Esophageal cancer esophageal cancer 1,017,445
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018479/ScoringFiles/PGS018479.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 —
PPM022397 PGS005160
(PRS-ESC)
 PSS011937|
East Asian Ancestry|
100,219 individuals
 PGP000711 |
Zhu M et al. PLoS Med (2025)
 Reported Trait: Esophageal Cancer HR: 1.26 [1.16, 1.38]
β: 0.246		 C-index: 0.559 — Age,Sex (if applicable),Region,Top 10 genetic ancestry principal components The HR and C-index values were derived from Cox proportional hazards regression models.
PPM036657 PGS018475
(TPMI_150_Lassosum2)
 PSS012378|
East Asian Ancestry|
15,479 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of esophagus — AUROC: 0.67404 R²: 0.00986 sex, age, array, PCs 1-10 —
PPM036658 PGS018476
(TPMI_150_LDpred2)
 PSS012377|
East Asian Ancestry|
15,479 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of esophagus — AUROC: 0.67403 R²: 0.00995 sex, age, array, PCs 1-10 —
PPM036659 PGS018477
(TPMI_150_MegaPRS)
 PSS012379|
East Asian Ancestry|
15,479 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of esophagus — AUROC: 0.67808 R²: 0.01048 sex, age, array, PCs 1-10 —
PPM036660 PGS018478
(TPMI_150_PRS-CS)
 PSS012380|
East Asian Ancestry|
15,479 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of esophagus — AUROC: 0.67763 R²: 0.01012 sex, age, array, PCs 1-10 —
PPM036661 PGS018479
(TPMI_150_SBayesR)
 PSS012381|
East Asian Ancestry|
15,479 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of esophagus — AUROC: 0.67327 R²: 0.00967 sex, age, array, PCs 1-10 —

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
PSS012381 150, 230.1, V10.03,C15, D00.1, Z85.01 —
[
  • 157 cases
  • , 15,322 controls
]
,
43.41 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS011937 ICD-10: C15 Median = 11.33 years
Range = [10.18, 12.26] years
[
  • 499 cases
  • , 99,720 controls
]
,
42.8 % Male samples
 Mean = 53.69 years
Sd = 11.01 years		 East Asian
(Chinese)		 — CKB —
PSS009661 esophageal cancer (ICD-9 = 150 or ICD-10 = C15) — 406 individuals — European — UKB —
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
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 —
PSS012377 150, 230.1, V10.03,C15, D00.1, Z85.01 —
[
  • 157 cases
  • , 15,322 controls
]
,
43.41 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012378 150, 230.1, V10.03,C15, D00.1, Z85.01 —
[
  • 157 cases
  • , 15,322 controls
]
,
43.41 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012379 150, 230.1, V10.03,C15, D00.1, Z85.01 —
[
  • 157 cases
  • , 15,322 controls
]
,
43.41 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012380 150, 230.1, V10.03,C15, D00.1, Z85.01 —
[
  • 157 cases
  • , 15,322 controls
]
,
43.41 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —