Polygenic Score (PGS) ID: PGS001099

Predicted Trait
Reported Trait Spherical power (left eye)
Mapped Trait(s) refractive error measurement (EFO_0007814)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5085
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_INI5085
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,639
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
65,996 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
65,996 individuals European white British ancestry UKB

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
PPM008234 PSS007371|
African Ancestry|
3,300 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Spherical power (L) : 0.04061 [0.03121, 0.05001]
Incremental R2 (full-covars): 0.00835
PGS R2 (no covariates): 0.01458 [0.00879, 0.02036]
age, sex, UKB array type, Genotype PCs
PPM008235 PSS007372|
East Asian Ancestry|
596 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Spherical power (L) : 0.09829 [0.0715, 0.12508]
Incremental R2 (full-covars): 0.01659
PGS R2 (no covariates): 0.0261 [0.01119, 0.04101]
age, sex, UKB array type, Genotype PCs
PPM008236 PSS007373|
European Ancestry|
7,900 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Spherical power (L) : 0.10172 [0.09461, 0.10884]
Incremental R2 (full-covars): 0.07033
PGS R2 (no covariates): 0.0711 [0.06495, 0.07725]
age, sex, UKB array type, Genotype PCs
PPM008237 PSS007374|
South Asian Ancestry|
3,648 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Spherical power (L) : 0.05929 [0.04915, 0.06943]
Incremental R2 (full-covars): 0.03026
PGS R2 (no covariates): 0.03238 [0.02467, 0.04009]
age, sex, UKB array type, Genotype PCs
PPM008238 PSS007375|
European Ancestry|
16,473 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Spherical power (L) : 0.11149 [0.10701, 0.11597]
Incremental R2 (full-covars): 0.09163
PGS R2 (no covariates): 0.09194 [0.08779, 0.0961]
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
PSS007371 3,300 individuals African unspecified UKB
PSS007372 596 individuals East Asian UKB
PSS007373 7,900 individuals European non-white British ancestry UKB
PSS007374 3,648 individuals South Asian UKB
PSS007375 16,473 individuals European white British ancestry UKB Testing cohort (heldout set)