Polygenic Score (PGS) ID: PGS002140

Predicted Trait
Reported Trait Wears glasses or contact lenses
Mapped Trait(s) eye measurement (EFO_0004731)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_glasses
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 762,684
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011967 PSS009410|
European Ancestry|
19,975 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0325 [0.0186, 0.0463] sex, age, birth date, deprivation index, 16 PCs —
PPM011968 PSS009184|
European Ancestry|
4,116 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0219 [-0.0087, 0.0525] sex, age, birth date, deprivation index, 16 PCs —
PPM011969 PSS008738|
European Ancestry|
6,627 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0514 [0.0273, 0.0754] sex, age, birth date, deprivation index, 16 PCs —
PPM011970 PSS008512|
Greater Middle Eastern Ancestry|
1,152 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0617 [0.0034, 0.1195] sex, age, birth date, deprivation index, 16 PCs —
PPM011971 PSS008290|
South Asian Ancestry|
6,213 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0358 [0.0109, 0.0606] sex, age, birth date, deprivation index, 16 PCs —
PPM011972 PSS008067|
East Asian Ancestry|
1,787 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0186 [-0.028, 0.0652] sex, age, birth date, deprivation index, 16 PCs —
PPM011973 PSS007854|
African Ancestry|
2,456 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0128 [-0.0269, 0.0525] sex, age, birth date, deprivation index, 16 PCs —
PPM011974 PSS008958|
African Ancestry|
3,859 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Wears glasses or contact lenses — — Partial Correlation (partial-r): 0.0247 [-0.007, 0.0562] sex, age, birth date, deprivation index, 16 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
PSS009410 — — 19,975 individuals — European UK (+ Ireland) UKB —
PSS007854 — — 2,456 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009184 — — 4,116 individuals — European Poland (NE Europe) UKB —
PSS008958 — — 3,859 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008290 — — 6,213 individuals — South Asian India (South Asia) UKB —
PSS008512 — — 1,152 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008738 — — 6,627 individuals — European Italy (South Europe) UKB —
PSS008067 — — 1,787 individuals — East Asian China (East Asia) UKB —