Polygenic Score (PGS) ID: PGS002103

Predicted Trait
Reported Trait avMSE
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-ldpred2_avMSE
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 833,170
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
PPM011680 PSS009386|
European Ancestry|
4,208 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3473 [0.3203, 0.3736] sex, age, birth date, deprivation index, 16 PCs —
PPM011681 PSS009160|
European Ancestry|
1,144 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3219 [0.2685, 0.3734] sex, age, birth date, deprivation index, 16 PCs —
PPM011682 PSS008714|
European Ancestry|
2,005 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2905 [0.2497, 0.3303] sex, age, birth date, deprivation index, 16 PCs —
PPM011683 PSS008488|
Greater Middle Eastern Ancestry|
440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2346 [0.1421, 0.3231] sex, age, birth date, deprivation index, 16 PCs —
PPM011684 PSS008266|
South Asian Ancestry|
2,632 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2366 [0.2001, 0.2725] sex, age, birth date, deprivation index, 16 PCs —
PPM011685 PSS008044|
East Asian Ancestry|
634 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.1513 [0.073, 0.2277] sex, age, birth date, deprivation index, 16 PCs —
PPM011687 PSS008934|
African Ancestry|
1,910 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.0959 [0.051, 0.1404] sex, age, birth date, deprivation index, 16 PCs —
PPM011686 PSS007830|
African Ancestry|
1,331 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.0923 [0.0384, 0.1457] 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
PSS008934 — — 1,910 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008488 — — 440 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009160 — — 1,144 individuals — European Poland (NE Europe) UKB —
PSS008714 — — 2,005 individuals — European Italy (South Europe) UKB —
PSS008266 — — 2,632 individuals — South Asian India (South Asia) UKB —
PSS009386 — — 4,208 individuals — European UK (+ Ireland) UKB —
PSS008044 — — 634 individuals — East Asian China (East Asia) UKB —
PSS007830 — — 1,331 individuals — African American or Afro-Caribbean Carribean UKB —