Polygenic Score (PGS) ID: PGS001013

Predicted Trait
Reported Trait Macular degeneration
Mapped Trait(s) macular degeneration (EFO_0009606)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC5006148
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_FC5006148
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 53
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%
88,703 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
—
[
  • 2,595 cases
  • , 86,108 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
PPM007828 PSS003974|
African Ancestry|
3,196 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.7052 [0.63504, 0.77537] R²: 0.07369
Incremental AUROC (full-covars): -0.00271
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.50582 [0.43466, 0.57699]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007829 PSS003975|
East Asian Ancestry|
711 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.90123 [0.8354, 0.96707] R²: 0.32752
Incremental AUROC (full-covars): -0.00016
PGS R2 (no covariates): 0.01068
PGS AUROC (no covariates): 0.59339 [0.45683, 0.72996]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007830 PSS003976|
European Ancestry|
9,755 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.72878 [0.69745, 0.76011] R²: 0.07729
Incremental AUROC (full-covars): 0.00516
PGS R2 (no covariates): 0.00265
PGS AUROC (no covariates): 0.53845 [0.49847, 0.57843]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007831 PSS003977|
South Asian Ancestry|
3,327 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.76624 [0.71098, 0.8215] R²: 0.10324
Incremental AUROC (full-covars): -0.00396
PGS R2 (no covariates): 0.00053
PGS AUROC (no covariates): 0.47169 [0.39626, 0.54712]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007832 PSS003978|
European Ancestry|
22,208 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.70257 [0.6826, 0.72253] R²: 0.06704
Incremental AUROC (full-covars): 0.00573
PGS R2 (no covariates): 0.00599
PGS AUROC (no covariates): 0.55283 [0.52939, 0.57627]		 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
PSS003974 — —
[
  • 68 cases
  • , 3,128 controls
]
 — African unspecified — UKB —
PSS003975 — —
[
  • 18 cases
  • , 693 controls
]
 — East Asian — UKB —
PSS003976 — —
[
  • 235 cases
  • , 9,520 controls
]
 — European non-white British ancestry UKB —
PSS003977 — —
[
  • 63 cases
  • , 3,264 controls
]
 — South Asian — UKB —
PSS003978 — —
[
  • 637 cases
  • , 21,571 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)