Polygenic Score (PGS) ID: PGS001363

Predicted Trait
Reported Trait 3mm weak meridian (R)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5099
Released in PGS Catalog: Nov. 25, 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_INI5099
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,983
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%
63,859 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
63,859 individuals European white British ancestry UKB Training + validation cohort (train_val)

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
PPM007147 PSS007393|
European Ancestry|
7,490 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm weak meridian (R) : 0.20585 [0.1969, 0.2148]
Incremental R2 (full-covars): 0.15187
PGS R2 (no covariates): 0.15592 [0.14764, 0.1642]
age, sex, UKB array type, Genotype PCs
PPM007148 PSS007394|
South Asian Ancestry|
3,448 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm weak meridian (R) : 0.18154 [0.1661, 0.19698]
Incremental R2 (full-covars): 0.10024
PGS R2 (no covariates): 0.10364 [0.09086, 0.11641]
age, sex, UKB array type, Genotype PCs
PPM007149 PSS007395|
European Ancestry|
15,963 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm weak meridian (R) : 0.21427 [0.20878, 0.21976]
Incremental R2 (full-covars): 0.17021
PGS R2 (no covariates): 0.16752 [0.16238, 0.17267]
age, sex, UKB array type, Genotype PCs
PPM007145 PSS007391|
African Ancestry|
3,083 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm weak meridian (R) : 0.10197 [0.08803, 0.11591]
Incremental R2 (full-covars): 0.02049
PGS R2 (no covariates): 0.02612 [0.01847, 0.03377]
age, sex, UKB array type, Genotype PCs
PPM007146 PSS007392|
East Asian Ancestry|
561 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm weak meridian (R) : 0.14867 [0.11756, 0.17978]
Incremental R2 (full-covars): 0.08784
PGS R2 (no covariates): 0.10479 [0.07733, 0.13226]
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
PSS007391 3,083 individuals African unspecified UKB
PSS007392 561 individuals East Asian UKB
PSS007393 7,490 individuals European non-white British ancestry UKB
PSS007394 3,448 individuals South Asian UKB
PSS007395 15,963 individuals European white British ancestry UKB Testing cohort (heldout set)