Polygenic Score (PGS) ID: PGS001366

Predicted Trait
Reported Trait 6mm strong meridian (R)
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5133
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_INI5133
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,219
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
PPM007170 PSS007421|
African Ancestry|
2,479 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (R) : 0.08936 [0.07613, 0.10259]
Incremental R2 (full-covars): 0.02587
PGS R2 (no covariates): 0.02944 [0.02135, 0.03754]
age, sex, UKB array type, Genotype PCs
PPM007171 PSS007422|
East Asian Ancestry|
464 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (R) : 0.18151 [0.14847, 0.21456]
Incremental R2 (full-covars): 0.11314
PGS R2 (no covariates): 0.12907 [0.09942, 0.15872]
age, sex, UKB array type, Genotype PCs
PPM007172 PSS007423|
European Ancestry|
6,613 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (R) : 0.21308 [0.20405, 0.2221]
Incremental R2 (full-covars): 0.15301
PGS R2 (no covariates): 0.1575 [0.14919, 0.1658]
age, sex, UKB array type, Genotype PCs
PPM007173 PSS007424|
South Asian Ancestry|
2,955 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (R) : 0.19615 [0.18038, 0.21191]
Incremental R2 (full-covars): 0.1069
PGS R2 (no covariates): 0.11348 [0.10025, 0.1267]
age, sex, UKB array type, Genotype PCs
PPM007174 PSS007425|
European Ancestry|
14,037 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: 6mm strong meridian (R) : 0.22083 [0.2153, 0.22636]
Incremental R2 (full-covars): 0.16703
PGS R2 (no covariates): 0.16537 [0.16025, 0.1705]
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
PSS007421 2,479 individuals African unspecified UKB
PSS007422 464 individuals East Asian UKB
PSS007423 6,613 individuals European non-white British ancestry UKB
PSS007424 2,955 individuals South Asian UKB
PSS007425 14,037 individuals European white British ancestry UKB Testing cohort (heldout set)