Polygenic Score (PGS) ID: PGS001364

Predicted Trait
Reported Trait 6mm cylindrical power angle (L)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5113
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_INI5113
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 319
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%
55,265 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
55,265 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
PPM007155 PSS007406|
African Ancestry|
2,562 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm cylindrical power angle (L) : 0.01042 [0.00551, 0.01532]
Incremental R2 (full-covars): 0.00093
PGS R2 (no covariates): 0.00146 [-0.0004, 0.00331]
age, sex, UKB array type, Genotype PCs
PPM007156 PSS007407|
East Asian Ancestry|
488 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm cylindrical power angle (L) : 0.00399 [-0.00197, 0.00996]
Incremental R2 (full-covars): -0.00511
PGS R2 (no covariates): 0.00661 [-0.00104, 0.01427]
age, sex, UKB array type, Genotype PCs
PPM007157 PSS007408|
European Ancestry|
6,612 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm cylindrical power angle (L) : 0.00307 [0.0017, 0.00444]
Incremental R2 (full-covars): 7e-05
PGS R2 (no covariates): 0.00021 [-0.00015, 0.00056]
age, sex, UKB array type, Genotype PCs
PPM007158 PSS007409|
South Asian Ancestry|
2,974 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm cylindrical power angle (L) : 0.00441 [0.00148, 0.00734]
Incremental R2 (full-covars): 0.00079
PGS R2 (no covariates): 0.00074 [-0.00046, 0.00195]
age, sex, UKB array type, Genotype PCs
PPM007159 PSS007410|
European Ancestry|
13,819 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm cylindrical power angle (L) : 0.00293 [0.00212, 0.00375]
Incremental R2 (full-covars): 0.00178
PGS R2 (no covariates): 0.00179 [0.00116, 0.00243]
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
PSS007406 2,562 individuals African unspecified UKB
PSS007407 488 individuals East Asian UKB
PSS007408 6,612 individuals European non-white British ancestry UKB
PSS007409 2,974 individuals South Asian UKB
PSS007410 13,819 individuals European white British ancestry UKB Testing cohort (heldout set)