Trait: esophageal disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009544
Description A non-neoplastic or neoplastic disorder that affects the esophagus. Representative examples of non-neoplastic disorders include esophagitis and esophageal ulcer. Representative examples of neoplastic disorders include carcinomas, lymphomas, and melanomas. [NCIT: C3027]
Trait category
Digestive system disorder
Synonyms 12 synonyms
  • disease of esophagus
  • disease of oesophagus
  • disease or disorder of esophagus
  • disease or disorder of oesophagus
  • disorder of esophagus
  • disorder of oesophagus
  • esophageal disorder
  • esophageal ulcer
  • esophagus disease
  • esophagus disease or disorder
  • oesophagus disease
  • oesophagus disease or disorder
Mapped terms 15 mapped terms
  • DOID:6050
  • ICD10:K22
  • ICD10:K22.9
  • ICD9:530
  • ICD9:530.2
  • ICD9:530.20
  • ICD9:530.9
  • MESH:D004935
  • MONDO:0003749
  • MeSH:D004935
  • NCIT:C3027
  • NCIt:C3027
  • SCTID:30811009
  • SCTID:37657006
  • UMLS:C0014852
Child trait(s) 6 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 disease" 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
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
PGS001851
(portability-PLR_530.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Esophagitis, GERD and related diseases gastroesophageal reflux disease,
esophagitis		 13,855
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001851/ScoringFiles/PGS001851.txt.gz
PGS002063
(portability-ldpred2_530.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Esophagitis, GERD and related diseases gastroesophageal reflux disease,
esophagitis		 836,413
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002063/ScoringFiles/PGS002063.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
PGS004468
(disease.K21.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 K21 (Gastroesophageal reflux disease) gastroesophageal reflux disease 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004468/ScoringFiles/PGS004468.txt.gz
PGS004469
(disease.K22.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 K22 (Other diseases of oesophagus) esophageal disease 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004469/ScoringFiles/PGS004469.txt.gz
PGS004538
(meta.K21.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 K21 (Gastroesophageal reflux disease) gastroesophageal reflux disease 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004538/ScoringFiles/PGS004538.txt.gz
PGS004539
(meta.K22.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 K22 (Other diseases of oesophagus) esophageal disease 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004539/ScoringFiles/PGS004539.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
PPM009698 PGS001851
(portability-PLR_530.1)
 PSS009326|
European Ancestry|
19,594 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.047 [0.033, 0.0609] sex, age, birth date, deprivation index, 16 PCs —
PPM009699 PGS001851
(portability-PLR_530.1)
 PSS009100|
European Ancestry|
4,045 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0513 [0.0205, 0.0821] sex, age, birth date, deprivation index, 16 PCs —
PPM009700 PGS001851
(portability-PLR_530.1)
 PSS008654|
European Ancestry|
6,525 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0309 [0.0066, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM009701 PGS001851
(portability-PLR_530.1)
 PSS008428|
Greater Middle Eastern Ancestry|
1,165 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0366 [-0.0214, 0.0943] sex, age, birth date, deprivation index, 16 PCs —
PPM009702 PGS001851
(portability-PLR_530.1)
 PSS008208|
South Asian Ancestry|
6,172 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0278 [0.0028, 0.0527] sex, age, birth date, deprivation index, 16 PCs —
PPM009703 PGS001851
(portability-PLR_530.1)
 PSS007990|
East Asian Ancestry|
1,774 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0121 [-0.0348, 0.0588] sex, age, birth date, deprivation index, 16 PCs —
PPM009704 PGS001851
(portability-PLR_530.1)
 PSS007773|
African Ancestry|
2,440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0244 [-0.0154, 0.0642] sex, age, birth date, deprivation index, 16 PCs —
PPM009705 PGS001851
(portability-PLR_530.1)
 PSS008877|
African Ancestry|
3,836 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0371 [0.0054, 0.0688] sex, age, birth date, deprivation index, 16 PCs —
PPM011366 PGS002063
(portability-ldpred2_530.1)
 PSS009326|
European Ancestry|
19,594 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0644 [0.0504, 0.0783] sex, age, birth date, deprivation index, 16 PCs —
PPM011367 PGS002063
(portability-ldpred2_530.1)
 PSS009100|
European Ancestry|
4,045 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0532 [0.0223, 0.084] sex, age, birth date, deprivation index, 16 PCs —
PPM011368 PGS002063
(portability-ldpred2_530.1)
 PSS008654|
European Ancestry|
6,525 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0447 [0.0204, 0.0689] sex, age, birth date, deprivation index, 16 PCs —
PPM011369 PGS002063
(portability-ldpred2_530.1)
 PSS008428|
Greater Middle Eastern Ancestry|
1,165 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0342 [-0.0238, 0.092] sex, age, birth date, deprivation index, 16 PCs —
PPM011370 PGS002063
(portability-ldpred2_530.1)
 PSS008208|
South Asian Ancestry|
6,172 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0522 [0.0273, 0.0771] sex, age, birth date, deprivation index, 16 PCs —
PPM011371 PGS002063
(portability-ldpred2_530.1)
 PSS007990|
East Asian Ancestry|
1,774 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0273 [-0.0196, 0.074] sex, age, birth date, deprivation index, 16 PCs —
PPM011372 PGS002063
(portability-ldpred2_530.1)
 PSS007773|
African Ancestry|
2,440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.034 [-0.0059, 0.0737] sex, age, birth date, deprivation index, 16 PCs —
PPM011373 PGS002063
(portability-ldpred2_530.1)
 PSS008877|
African Ancestry|
3,836 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0136 [-0.0181, 0.0454] sex, age, birth date, deprivation index, 16 PCs —
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 —
PPM020583 PGS004468
(disease.K21.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: K21 (Gastro-oesophageal reflux disease) OR: 1.19096 — — — —
PPM020584 PGS004469
(disease.K22.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: K22 (Other diseases of oesophagus) OR: 1.1802 — — — —
PPM020653 PGS004538
(meta.K21.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: K21 (Gastro-oesophageal reflux disease) OR: 1.26524 — — — —
PPM020654 PGS004539
(meta.K22.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: K22 (Other diseases of oesophagus) OR: 1.20366 — — — —

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
PSS009661 esophageal cancer (ICD-9 = 150 or ICD-10 = C15) — 406 individuals — European — UKB —
PSS009100 — — 4,045 individuals — European Poland (NE Europe) UKB —
PSS008428 — — 1,165 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009326 — — 19,594 individuals — European UK (+ Ireland) UKB —
PSS008654 — — 6,525 individuals — European Italy (South Europe) UKB —
PSS008208 — — 6,172 individuals — South Asian India (South Asia) UKB —
PSS008877 — — 3,836 individuals — African unspecified Nigeria (West Africa) 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 —
PSS007990 — — 1,774 individuals — East Asian China (East Asia) UKB —
PSS007773 — — 2,440 individuals — African American or Afro-Caribbean Carribean UKB —
PSS011364 — — 56,192 individuals — European — UKB —