Polygenic Score (PGS) ID: PGS001985

Predicted Trait
Reported Trait logMAR in round (left/right)
Mapped Trait(s) visual acuity measurement (EFO_0008385)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
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 portability-PLR_logMAR
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 223
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010755 PSS009425|
European Ancestry|
4,973 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0683 [0.0405, 0.0959] sex, age, birth date, deprivation index, 16 PCs
PPM010757 PSS008753|
European Ancestry|
2,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0178 [-0.0242, 0.0598] sex, age, birth date, deprivation index, 16 PCs
PPM010758 PSS008527|
Greater Middle Eastern Ancestry|
473 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0533 [-0.039, 0.1447] sex, age, birth date, deprivation index, 16 PCs
PPM010759 PSS008305|
South Asian Ancestry|
2,803 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): -0.0076 [-0.0447, 0.0296] sex, age, birth date, deprivation index, 16 PCs
PPM010760 PSS008082|
East Asian Ancestry|
698 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): -0.0376 [-0.1126, 0.0378] sex, age, birth date, deprivation index, 16 PCs
PPM010761 PSS007869|
African Ancestry|
1,407 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0259 [-0.0268, 0.0784] sex, age, birth date, deprivation index, 16 PCs
PPM010762 PSS008973|
African Ancestry|
2,025 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): -0.0189 [-0.0627, 0.0249] sex, age, birth date, deprivation index, 16 PCs
PPM010756 PSS009199|
European Ancestry|
1,340 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0299 [-0.0241, 0.0837] 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
PSS008973 2,025 individuals African unspecified Nigeria (West Africa) UKB
PSS008527 473 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009199 1,340 individuals European Poland (NE Europe) UKB
PSS008305 2,803 individuals South Asian India (South Asia) UKB
PSS009425 4,973 individuals European UK (+ Ireland) UKB
PSS008082 698 individuals East Asian China (East Asia) UKB
PSS008753 2,200 individuals European Italy (South Europe) UKB
PSS007869 1,407 individuals African American or Afro-Caribbean Carribean UKB