Polygenic Score (PGS) ID: PGS001100

Predicted Trait
Reported Trait Spherical power (right eye)
Mapped Trait(s) refractive error measurement (EFO_0007814)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5084
Released in PGS Catalog: Oct. 21, 2021
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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_INI5084
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,350
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%
66,193 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
— 66,193 individuals 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
PPM008239 PSS007366|
African Ancestry|
3,314 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Spherical power (R) — — R²: 0.03542 [0.02659, 0.04424]
Incremental R2 (full-covars): 0.00616
PGS R2 (no covariates): 0.01203 [0.00676, 0.0173]		 age, sex, UKB array type, Genotype PCs —
PPM008240 PSS007367|
East Asian Ancestry|
597 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Spherical power (R) — — R²: 0.1128 [0.08456, 0.14104]
Incremental R2 (full-covars): 0.02771
PGS R2 (no covariates): 0.03839 [0.02053, 0.05624]		 age, sex, UKB array type, Genotype PCs —
PPM008241 PSS007368|
European Ancestry|
7,920 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Spherical power (R) — — R²: 0.10687 [0.09962, 0.11412]
Incremental R2 (full-covars): 0.07031
PGS R2 (no covariates): 0.0711 [0.06495, 0.07725]		 age, sex, UKB array type, Genotype PCs —
PPM008242 PSS007369|
South Asian Ancestry|
3,663 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Spherical power (R) — — R²: 0.06585 [0.05523, 0.07646]
Incremental R2 (full-covars): 0.0281
PGS R2 (no covariates): 0.03071 [0.02319, 0.03823]		 age, sex, UKB array type, Genotype PCs —
PPM008243 PSS007370|
European Ancestry|
16,545 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Spherical power (R) — — R²: 0.11691 [0.11236, 0.12147]
Incremental R2 (full-covars): 0.0945
PGS R2 (no covariates): 0.09518 [0.09097, 0.0994]		 age, sex, UKB array type, Genotype PCs —

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
PSS007366 — — 3,314 individuals — African unspecified — UKB —
PSS007367 — — 597 individuals — East Asian — UKB —
PSS007368 — — 7,920 individuals — European non-white British ancestry UKB —
PSS007369 — — 3,663 individuals — South Asian — UKB —
PSS007370 — — 16,545 individuals — European white British ancestry UKB Testing cohort (heldout set)