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
  • ICD9:371.30
  • ICD9:371.89
  • ICD9:371.9
  • MEDGEN:3617
  • MESH:D003316
  • MONDO:0000942
  • NCIT:C26731
  • NCIt:C26731
  • SCTID:15250008
  • UMLS:C0010034
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 "corneal 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)
PGS001029
(GBE_HC866)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 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
PGS001835
(portability-PLR_364.5)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Corneal dystrophy corneal dystrophy 38
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001835/ScoringFiles/PGS001835.txt.gz
PGS002042
(portability-ldpred2_364.5)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Corneal dystrophy corneal dystrophy 59,944
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002042/ScoringFiles/PGS002042.txt.gz
PGS002292
(PRS36_KC)
 PGP000321 |
He W et al. JAMA Ophthalmol (2022)
 Keratoconus keratoconus 36
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002292/ScoringFiles/PGS002292.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. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.71052 [0.62918, 0.79186] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.48912 [0.0043, 0.97395] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.63469 [0.57721, 0.69216] PGS R2 (no covariates): 0.01229
R²: 0.01902
Incremental AUROC (full-covars): 0.04837
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. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.62122 [0.5586, 0.68385] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.60075 [0.56985, 0.63165] R²: 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
PPM009572 PGS001835
(portability-PLR_364.5)
 PSS009305|
European Ancestry|
19,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0384 [0.0243, 0.0525] sex, age, birth date, deprivation index, 16 PCs —
PPM009573 PGS001835
(portability-PLR_364.5)
 PSS009079|
European Ancestry|
4,029 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0753 [0.0445, 0.106] sex, age, birth date, deprivation index, 16 PCs —
PPM009574 PGS001835
(portability-PLR_364.5)
 PSS008633|
European Ancestry|
6,462 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0488 [0.0245, 0.0732] sex, age, birth date, deprivation index, 16 PCs —
PPM009575 PGS001835
(portability-PLR_364.5)
 PSS008407|
Greater Middle Eastern Ancestry|
1,162 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0128 [-0.0452, 0.0708] sex, age, birth date, deprivation index, 16 PCs —
PPM009577 PGS001835
(portability-PLR_364.5)
 PSS008857|
African Ancestry|
3,718 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): -0.0168 [-0.049, 0.0155] sex, age, birth date, deprivation index, 16 PCs —
PPM009576 PGS001835
(portability-PLR_364.5)
 PSS008187|
South Asian Ancestry|
6,052 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): -0.011 [-0.0362, 0.0143] sex, age, birth date, deprivation index, 16 PCs —
PPM011202 PGS002042
(portability-ldpred2_364.5)
 PSS009305|
European Ancestry|
19,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0471 [0.033, 0.0611] sex, age, birth date, deprivation index, 16 PCs —
PPM011203 PGS002042
(portability-ldpred2_364.5)
 PSS009079|
European Ancestry|
4,029 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0812 [0.0504, 0.1119] sex, age, birth date, deprivation index, 16 PCs —
PPM011204 PGS002042
(portability-ldpred2_364.5)
 PSS008633|
European Ancestry|
6,462 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0519 [0.0275, 0.0762] sex, age, birth date, deprivation index, 16 PCs —
PPM011205 PGS002042
(portability-ldpred2_364.5)
 PSS008407|
Greater Middle Eastern Ancestry|
1,162 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0275 [-0.0306, 0.0853] sex, age, birth date, deprivation index, 16 PCs —
PPM011206 PGS002042
(portability-ldpred2_364.5)
 PSS008187|
South Asian Ancestry|
6,052 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): -0.0133 [-0.0385, 0.0119] sex, age, birth date, deprivation index, 16 PCs —
PPM011207 PGS002042
(portability-ldpred2_364.5)
 PSS008857|
African Ancestry|
3,718 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): -0.0084 [-0.0406, 0.0238] sex, age, birth date, deprivation index, 16 PCs —
PPM013012 PGS002292
(PRS36_KC)
 PSS009647|
European Ancestry|
142,595 individuals
 PGP000321 |
He W et al. JAMA Ophthalmol (2022)
 Reported Trait: Keratoconus — AUROC: 0.705 — — —
PPM013013 PGS002292
(PRS36_KC)
 PSS009647|
European Ancestry|
142,595 individuals
 PGP000321 |
He W et al. JAMA Ophthalmol (2022)
 Reported Trait: Keratoconus with corneal resistance factor variants — AUROC: 0.756 — — —
PPM013014 PGS002292
(PRS36_KC)
 PSS009647|
European Ancestry|
142,595 individuals
 PGP000321 |
He W et al. JAMA Ophthalmol (2022)
 Reported Trait: Keratoconus with central corneal thickness variants — AUROC: 0.755 — — —

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
PSS009647 Keratoconus cases (ICD10 diagnosis code H186) and healthy controls without severe eye diseases (UKB Field 6148) —
[
  • 102 cases
  • , 142,493 controls
]
 — European — UKB —
PSS009079 — — 4,029 individuals — European Poland (NE Europe) UKB —
PSS008407 — — 1,162 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009305 — — 19,321 individuals — European UK (+ Ireland) UKB —
PSS008633 — — 6,462 individuals — European Italy (South Europe) UKB —
PSS008857 — — 3,718 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008187 — — 6,052 individuals — South Asian India (South Asia) UKB —
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)