Polygenic Score (PGS) ID: PGS001368

Predicted Trait
Reported Trait 6mm weak meridian (R)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5098
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_INI5098
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,730
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%
56,012 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
56,012 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
PPM007140 PSS007386|
African Ancestry|
2,479 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm weak meridian (R) : 0.09641 [0.08278, 0.11005]
Incremental R2 (full-covars): 0.03071
PGS R2 (no covariates): 0.0336 [0.02499, 0.0422]
age, sex, UKB array type, Genotype PCs
PPM007141 PSS007387|
East Asian Ancestry|
464 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm weak meridian (R) : 0.18894 [0.15553, 0.22235]
Incremental R2 (full-covars): 0.11067
PGS R2 (no covariates): 0.12478 [0.09548, 0.15408]
age, sex, UKB array type, Genotype PCs
PPM007142 PSS007388|
European Ancestry|
6,613 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm weak meridian (R) : 0.20364 [0.19472, 0.21257]
Incremental R2 (full-covars): 0.14383
PGS R2 (no covariates): 0.14815 [0.14001, 0.15629]
age, sex, UKB array type, Genotype PCs
PPM007143 PSS007389|
South Asian Ancestry|
2,955 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm weak meridian (R) : 0.21062 [0.19458, 0.22666]
Incremental R2 (full-covars): 0.11253
PGS R2 (no covariates): 0.12284 [0.10923, 0.13645]
age, sex, UKB array type, Genotype PCs
PPM007144 PSS007390|
European Ancestry|
14,037 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm weak meridian (R) : 0.22246 [0.21692, 0.228]
Incremental R2 (full-covars): 0.17034
PGS R2 (no covariates): 0.16779 [0.16264, 0.17293]
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
PSS007388 6,613 individuals European non-white British ancestry UKB
PSS007389 2,955 individuals South Asian UKB
PSS007390 14,037 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS007386 2,479 individuals African unspecified UKB
PSS007387 464 individuals East Asian UKB