Polygenic Score (PGS) ID: PGS001359

Predicted Trait
Reported Trait 3mm strong meridian (L)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5135
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_INI5135
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,497
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%
63,875 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
63,875 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
PPM007184 PSS007435|
European Ancestry|
15,926 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (L) : 0.20335 [0.19793, 0.20877]
Incremental R2 (full-covars): 0.15243
PGS R2 (no covariates): 0.15093 [0.14595, 0.15591]
age, sex, UKB array type, Genotype PCs
PPM007180 PSS007431|
African Ancestry|
3,105 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (L) : 0.08579 [0.07278, 0.09881]
Incremental R2 (full-covars): 0.00558
PGS R2 (no covariates): 0.014 [0.00833, 0.01967]
age, sex, UKB array type, Genotype PCs
PPM007181 PSS007432|
East Asian Ancestry|
573 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (L) : 0.11668 [0.08808, 0.14527]
Incremental R2 (full-covars): 0.05741
PGS R2 (no covariates): 0.07134 [0.04783, 0.09485]
age, sex, UKB array type, Genotype PCs
PPM007182 PSS007433|
European Ancestry|
7,529 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (L) : 0.19283 [0.18403, 0.20164]
Incremental R2 (full-covars): 0.13671
PGS R2 (no covariates): 0.13985 [0.13186, 0.14784]
age, sex, UKB array type, Genotype PCs
PPM007183 PSS007434|
South Asian Ancestry|
3,455 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 3mm strong meridian (L) : 0.17172 [0.15653, 0.18692]
Incremental R2 (full-covars): 0.09777
PGS R2 (no covariates): 0.10232 [0.08961, 0.11503]
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
PSS007431 3,105 individuals African unspecified UKB
PSS007432 573 individuals East Asian UKB
PSS007433 7,529 individuals European non-white British ancestry UKB
PSS007434 3,455 individuals South Asian UKB
PSS007435 15,926 individuals European white British ancestry UKB Testing cohort (heldout set)