Polygenic Score (PGS) ID: PGS002211

Predicted Trait
Reported Trait Myopia diagnosis
Mapped Trait(s) Myopia (HP_0000545)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_myopia
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 825,631
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
PPM012535 PSS009477|
European Ancestry|
4,226 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.2603 [0.2319, 0.2882] sex, age, birth date, deprivation index, 16 PCs —
PPM012536 PSS009251|
European Ancestry|
1,151 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.255 [0.1997, 0.3087] sex, age, birth date, deprivation index, 16 PCs —
PPM012537 PSS008805|
European Ancestry|
2,021 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.2133 [0.1711, 0.2547] sex, age, birth date, deprivation index, 16 PCs —
PPM012538 PSS008579|
Greater Middle Eastern Ancestry|
441 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.1722 [0.0779, 0.2634] sex, age, birth date, deprivation index, 16 PCs —
PPM012540 PSS008134|
East Asian Ancestry|
649 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.1198 [0.042, 0.1961] sex, age, birth date, deprivation index, 16 PCs —
PPM012541 PSS007921|
African Ancestry|
1,344 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.0953 [0.0416, 0.1484] sex, age, birth date, deprivation index, 16 PCs —
PPM012542 PSS009025|
African Ancestry|
1,916 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.0638 [0.0189, 0.1085] sex, age, birth date, deprivation index, 16 PCs —
PPM012539 PSS008357|
South Asian Ancestry|
2,654 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Myopia diagnosis — — Partial Correlation (partial-r): 0.1654 [0.128, 0.2023] 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
PSS009477 — — 4,226 individuals — European UK (+ Ireland) UKB —
PSS008134 — — 649 individuals — East Asian China (East Asia) UKB —
PSS008805 — — 2,021 individuals — European Italy (South Europe) UKB —
PSS008357 — — 2,654 individuals — South Asian India (South Asia) UKB —
PSS007921 — — 1,344 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009025 — — 1,916 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009251 — — 1,151 individuals — European Poland (NE Europe) UKB —
PSS008579 — — 441 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —