Trait: corneal disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009464
Description A non-neoplastic or neoplastic disorder that affects the cornea. Representative examples include keratitis, bullous keratopathy, and squamous cell carcinoma. [NCIT: P378]
Trait category
Other disease
Synonyms 7 synonyms
  • cornea disease
  • cornea disease or disorder
  • corneal disease
  • corneal disorder
  • disease of cornea
  • disease or disorder of cornea
  • disorder of cornea
Mapped terms 11 mapped terms
  • DOID:10124
  • ICD10:H18.9
  • ICD9:371.30
  • ICD9:371.89
  • ICD9:371.9
  • MESH:D003316
  • MONDO:0000942
  • NCIT:C26731
  • NCIt:C26731
  • SCTID:15250008
  • UMLS:C0010034

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
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001029
(GBE_HC866)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Other disorders of cornea (time-to-event) corneal disease 22
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001029/ScoringFiles/PGS001029.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
PPM007908 PGS001029
(GBE_HC866)
PSS004662|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other disorders of cornea AUROC: 0.71052 [0.62918, 0.79186] : 0.05427
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00332
PGS AUROC (no covariates): 0.54756 [0.45415, 0.64098]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007909 PGS001029
(GBE_HC866)
PSS004663|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other disorders of cornea AUROC: 0.48912 [0.0043, 0.97395] : 0.00203
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.00633
PGS AUROC (no covariates): 0.40016 [0.0, 0.86755]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007910 PGS001029
(GBE_HC866)
PSS004664|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other disorders of cornea AUROC: 0.63469 [0.57721, 0.69216] : 0.01902
Incremental AUROC (full-covars): 0.04837
PGS R2 (no covariates): 0.01229
PGS AUROC (no covariates): 0.59818 [0.5417, 0.65467]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007911 PGS001029
(GBE_HC866)
PSS004665|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other disorders of cornea AUROC: 0.62122 [0.5586, 0.68385] : 0.02027
Incremental AUROC (full-covars): -0.01924
PGS R2 (no covariates): 0.00532
PGS AUROC (no covariates): 0.44761 [0.382, 0.51322]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007912 PGS001029
(GBE_HC866)
PSS004666|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other disorders of cornea AUROC: 0.60075 [0.56985, 0.63165] : 0.01227
Incremental AUROC (full-covars): 0.02429
PGS R2 (no covariates): 0.00807
PGS AUROC (no covariates): 0.58115 [0.55051, 0.61178]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004662
[
  • 34 cases
  • , 6,463 controls
]
African unspecified UKB
PSS004663
[
  • 3 cases
  • , 1,701 controls
]
East Asian UKB
PSS004664
[
  • 104 cases
  • , 24,801 controls
]
European non-white British ancestry UKB
PSS004665
[
  • 61 cases
  • , 7,770 controls
]
South Asian UKB
PSS004666
[
  • 353 cases
  • , 67,072 controls
]
European white British ancestry UKB Testing cohort (heldout set)