Polygenic Score (PGS) ID: PGS001358

Predicted Trait
Reported Trait 3mm cylindrical power (R)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5116
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_INI5116
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 148
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
PPM007160 PSS007411|
African Ancestry|
3,083 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm cylindrical power (R) : 0.00625 [0.00243, 0.01007]
Incremental R2 (full-covars): 0.00132
PGS R2 (no covariates): 0.00174 [-0.00028, 0.00376]
age, sex, UKB array type, Genotype PCs
PPM007161 PSS007412|
East Asian Ancestry|
561 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm cylindrical power (R) : 0.01957 [0.00657, 0.03257]
Incremental R2 (full-covars): 0.00157
PGS R2 (no covariates): 0.00123 [-0.00209, 0.00456]
age, sex, UKB array type, Genotype PCs
PPM007162 PSS007413|
European Ancestry|
7,490 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm cylindrical power (R) : 0.01243 [0.00969, 0.01516]
Incremental R2 (full-covars): 0.00335
PGS R2 (no covariates): 0.00413 [0.00254, 0.00572]
age, sex, UKB array type, Genotype PCs
PPM007163 PSS007414|
South Asian Ancestry|
3,448 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm cylindrical power (R) : 0.00875 [0.00465, 0.01286]
Incremental R2 (full-covars): 0.00126
PGS R2 (no covariates): 0.00125 [-0.00031, 0.00281]
age, sex, UKB array type, Genotype PCs
PPM007164 PSS007415|
European Ancestry|
15,963 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm cylindrical power (R) : 0.00746 [0.00617, 0.00876]
Incremental R2 (full-covars): 0.00253
PGS R2 (no covariates): 0.00262 [0.00185, 0.00339]
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
PSS007411 3,083 individuals African unspecified UKB
PSS007412 561 individuals East Asian UKB
PSS007413 7,490 individuals European non-white British ancestry UKB
PSS007414 3,448 individuals South Asian UKB
PSS007415 15,963 individuals European white British ancestry UKB Testing cohort (heldout set)