Polygenic Score (PGS) ID: PGS001365

Predicted Trait
Reported Trait 6mm strong meridian (L)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5134
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_INI5134
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,504
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%
55,283 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
55,283 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
PPM007175 PSS007426|
African Ancestry|
2,562 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (L) : 0.08943 [0.07619, 0.10267]
Incremental R2 (full-covars): 0.01354
PGS R2 (no covariates): 0.01781 [0.01144, 0.02418]
age, sex, UKB array type, Genotype PCs
PPM007176 PSS007427|
East Asian Ancestry|
488 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (L) : 0.16518 [0.13303, 0.19733]
Incremental R2 (full-covars): 0.09434
PGS R2 (no covariates): 0.11321 [0.08494, 0.14149]
age, sex, UKB array type, Genotype PCs
PPM007177 PSS007428|
European Ancestry|
6,614 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (L) : 0.21084 [0.20184, 0.21984]
Incremental R2 (full-covars): 0.14404
PGS R2 (no covariates): 0.15015 [0.14197, 0.15833]
age, sex, UKB array type, Genotype PCs
PPM007178 PSS007429|
South Asian Ancestry|
2,974 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (L) : 0.1943 [0.17858, 0.21003]
Incremental R2 (full-covars): 0.10957
PGS R2 (no covariates): 0.11731 [0.10392, 0.1307]
age, sex, UKB array type, Genotype PCs
PPM007179 PSS007430|
European Ancestry|
13,827 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (L) : 0.22292 [0.21738, 0.22846]
Incremental R2 (full-covars): 0.16477
PGS R2 (no covariates): 0.16497 [0.15985, 0.17009]
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
PSS007426 2,562 individuals African unspecified UKB
PSS007427 488 individuals East Asian UKB
PSS007428 6,614 individuals European non-white British ancestry UKB
PSS007429 2,974 individuals South Asian UKB
PSS007430 13,827 individuals European white British ancestry UKB Testing cohort (heldout set)