Polygenic Score (PGS) ID: PGS001360

Predicted Trait
Reported Trait 3mm strong meridian (R)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5132
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_INI5132
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 10,082
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
PPM007165 PSS007416|
African Ancestry|
3,083 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (R) : 0.09618 [0.08255, 0.1098]
Incremental R2 (full-covars): 0.01765
PGS R2 (no covariates): 0.02408 [0.01672, 0.03144]
age, sex, UKB array type, Genotype PCs
PPM007166 PSS007417|
East Asian Ancestry|
561 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (R) : 0.13087 [0.10107, 0.16067]
Incremental R2 (full-covars): 0.08472
PGS R2 (no covariates): 0.09914 [0.07226, 0.12602]
age, sex, UKB array type, Genotype PCs
PPM007167 PSS007418|
European Ancestry|
7,490 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (R) : 0.19721 [0.18836, 0.20607]
Incremental R2 (full-covars): 0.14384
PGS R2 (no covariates): 0.14672 [0.13861, 0.15484]
age, sex, UKB array type, Genotype PCs
PPM007168 PSS007419|
South Asian Ancestry|
3,448 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (R) : 0.17296 [0.15773, 0.18819]
Incremental R2 (full-covars): 0.10013
PGS R2 (no covariates): 0.1028 [0.09007, 0.11554]
age, sex, UKB array type, Genotype PCs
PPM007169 PSS007420|
European Ancestry|
15,963 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (R) : 0.20775 [0.2023, 0.2132]
Incremental R2 (full-covars): 0.15925
PGS R2 (no covariates): 0.15761 [0.15256, 0.16266]
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
PSS007420 15,963 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS007416 3,083 individuals African unspecified UKB
PSS007417 561 individuals East Asian UKB
PSS007418 7,490 individuals European non-white British ancestry UKB
PSS007419 3,448 individuals South Asian UKB