Polygenic Score (PGS) ID: PGS001373

Predicted Trait
Reported Trait Age started wearing glasses or contact lenses
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI2217
Released in PGS Catalog: Nov. 25, 2021
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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_INI2217
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,870
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%
235,611 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
235,611 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
PPM005295 PSS004961|
African Ancestry|
4,649 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age started wearing glasses or contact lenses : 0.1035 [0.08948, 0.11752]
Incremental R2 (full-covars): -0.00917
PGS R2 (no covariates): 0.00052 [-0.00059, 0.00163]
age, sex, UKB array type, Genotype PCs
PPM005296 PSS004962|
East Asian Ancestry|
1,320 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age started wearing glasses or contact lenses : 0.12386 [0.09464, 0.15308]
Incremental R2 (full-covars): 0.01011
PGS R2 (no covariates): 0.02059 [0.00727, 0.03391]
age, sex, UKB array type, Genotype PCs
PPM005297 PSS004963|
European Ancestry|
20,985 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age started wearing glasses or contact lenses : 0.09208 [0.08524, 0.09892]
Incremental R2 (full-covars): 0.02641
PGS R2 (no covariates): 0.02927 [0.02514, 0.03339]
age, sex, UKB array type, Genotype PCs
PPM005298 PSS004964|
South Asian Ancestry|
6,001 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age started wearing glasses or contact lenses : 0.10663 [0.09372, 0.11955]
Incremental R2 (full-covars): 0.0126
PGS R2 (no covariates): 0.0173 [0.01158, 0.02302]
age, sex, UKB array type, Genotype PCs
PPM005299 PSS004965|
European Ancestry|
58,837 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age started wearing glasses or contact lenses : 0.05662 [0.05323, 0.06001]
Incremental R2 (full-covars): 0.02363
PGS R2 (no covariates): 0.02425 [0.02196, 0.02655]
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
PSS004961 4,649 individuals African unspecified UKB
PSS004962 1,320 individuals East Asian UKB
PSS004963 20,985 individuals European non-white British ancestry UKB
PSS004964 6,001 individuals South Asian UKB
PSS004965 58,837 individuals European white British ancestry UKB Testing cohort (heldout set)