Polygenic Score (PGS) ID: PGS001028

Predicted Trait
Reported Trait Diabetic eye disease
Mapped Trait(s) diabetic eye disease (EFO_0009486)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1006148
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN_FC1006148
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 123
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
88,153 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 1,909 cases
  • , 86,244 controls
]
 European UKB — — — white British ancestry —

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) 		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 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 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 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 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 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

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
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)