Trait: diabetic eye disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009486
Description A group of disorders affecting the eye in patients with diabetes mellitus. It includes cataract, glaucoma, retinopathy, and blindness. [ NCI ]
Trait category
Other disease
Mapped terms 2 mapped terms
  • MedDRA:10012661
  • NCIt:C84420

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001028
(GBE_BIN_FC1006148)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Diabetic eye disease diabetic eye disease 123
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001028/ScoringFiles/PGS001028.txt.gz
PGS018758
(TPMI_250.23_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Type 2 diabetes with ophthalmic manifestations diabetic eye disease 7,766
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018758/ScoringFiles/PGS018758.txt.gz
PGS018759
(TPMI_250.23_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Type 2 diabetes with ophthalmic manifestations diabetic eye disease 939,826
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018759/ScoringFiles/PGS018759.txt.gz
PGS018760
(TPMI_250.23_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Type 2 diabetes with ophthalmic manifestations diabetic eye disease 159,132
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018760/ScoringFiles/PGS018760.txt.gz
PGS018761
(TPMI_250.23_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Type 2 diabetes with ophthalmic manifestations diabetic eye disease 983,777
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018761/ScoringFiles/PGS018761.txt.gz
PGS018762
(TPMI_250.23_PRSmix+)
 PGP000835 |
Chen HH et al. Nature (2025)
 Type 2 diabetes with ophthalmic manifestations diabetic eye disease 1,071,469
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018762/ScoringFiles/PGS018762.txt.gz
PGS018763
(TPMI_250.23_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Type 2 diabetes with ophthalmic manifestations diabetic eye disease 1,005,452
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018763/ScoringFiles/PGS018763.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
PPM007903 PGS001028
(GBE_BIN_FC1006148)
 PSS003765|
African Ancestry|
3,307 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Diabetic eye disease — AUROC: 0.76275 [0.72796, 0.79755] R²: 0.13906
Incremental AUROC (full-covars): 0.0014
PGS R2 (no covariates): 0.00197
PGS AUROC (no covariates): 0.53892 [0.49569, 0.58215]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007904 PGS001028
(GBE_BIN_FC1006148)
 PSS003766|
East Asian Ancestry|
706 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Diabetic eye disease — AUROC: 0.83123 [0.71584, 0.94663] R²: 0.24524
Incremental AUROC (full-covars): -0.00599
PGS R2 (no covariates): 0.0016
PGS AUROC (no covariates): 0.44953 [0.27083, 0.62822]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007905 PGS001028
(GBE_BIN_FC1006148)
 PSS003767|
European Ancestry|
9,719 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Diabetic eye disease — AUROC: 0.69201 [0.65353, 0.73049] R²: 0.05584
Incremental AUROC (full-covars): 0.01974
PGS R2 (no covariates): 0.01281
PGS AUROC (no covariates): 0.5903 [0.54859, 0.632]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007906 PGS001028
(GBE_BIN_FC1006148)
 PSS003768|
South Asian Ancestry|
3,533 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Diabetic eye disease — AUROC: 0.7302 [0.69952, 0.76088] Incremental AUROC (full-covars): 0.002
R²: 0.11745
PGS R2 (no covariates): 0.00272
PGS AUROC (no covariates): 0.53803 [0.50292, 0.57313]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007907 PGS001028
(GBE_BIN_FC1006148)
 PSS003769|
European Ancestry|
22,053 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Diabetic eye disease — AUROC: 0.69853 [0.67583, 0.72122] R²: 0.05279
Incremental AUROC (full-covars): 0.01792
PGS R2 (no covariates): 0.00926
PGS AUROC (no covariates): 0.57814 [0.55078, 0.6055]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM036940 PGS018758
(TPMI_250.23_Lassosum2)
 PSS012632|
East Asian Ancestry|
15,449 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Type 2 diabetes with ophthalmic manifestations — AUROC: 0.65648 R²: 0.03833 sex, age, array, PCs 1-10 —
PPM036941 PGS018759
(TPMI_250.23_LDpred2)
 PSS012631|
East Asian Ancestry|
15,449 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Type 2 diabetes with ophthalmic manifestations — AUROC: 0.67446 R²: 0.04798 sex, age, array, PCs 1-10 —
PPM036942 PGS018760
(TPMI_250.23_MegaPRS)
 PSS012633|
East Asian Ancestry|
15,449 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Type 2 diabetes with ophthalmic manifestations — AUROC: 0.65466 R²: 0.03786 sex, age, array, PCs 1-10 —
PPM036943 PGS018761
(TPMI_250.23_PRS-CS)
 PSS012634|
East Asian Ancestry|
15,449 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Type 2 diabetes with ophthalmic manifestations — AUROC: 0.671 R²: 0.04649 sex, age, array, PCs 1-10 —
PPM036944 PGS018762
(TPMI_250.23_PRSmix+)
 PSS012635|
East Asian Ancestry|
15,449 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Type 2 diabetes with ophthalmic manifestations — AUROC: 0.70717 R²: 0.06794 sex, age, array, PCs 1-10 —
PPM036945 PGS018763
(TPMI_250.23_SBayesR)
 PSS012636|
East Asian Ancestry|
15,449 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Type 2 diabetes with ophthalmic manifestations — AUROC: 0.65724 R²: 0.03763 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
PSS012633 250.50, 250.52,E11.3 —
[
  • 1,443 cases
  • , 14,006 controls
]
,
43.57 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012634 250.50, 250.52,E11.3 —
[
  • 1,443 cases
  • , 14,006 controls
]
,
43.57 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012635 250.50, 250.52,E11.3 —
[
  • 1,443 cases
  • , 14,006 controls
]
,
43.57 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012631 250.50, 250.52,E11.3 —
[
  • 1,443 cases
  • , 14,006 controls
]
,
43.57 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS003765 — —
[
  • 182 cases
  • , 3,125 controls
]
 — African unspecified — UKB —
PSS003766 — —
[
  • 14 cases
  • , 692 controls
]
 — East Asian — UKB —
PSS003767 — —
[
  • 187 cases
  • , 9,532 controls
]
 — European non-white British ancestry UKB —
PSS003768 — —
[
  • 269 cases
  • , 3,264 controls
]
 — South Asian — UKB —
PSS003769 — —
[
  • 444 cases
  • , 21,609 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS012632 250.50, 250.52,E11.3 —
[
  • 1,443 cases
  • , 14,006 controls
]
,
43.57 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012636 250.50, 250.52,E11.3 —
[
  • 1,443 cases
  • , 14,006 controls
]
,
43.57 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —