Polygenic Score (PGS) ID: PGS002044

Predicted Trait
Reported Trait Cataract
Mapped Trait(s) cataract (MONDO_0005129)
Additional Trait Information sense organs
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_366
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 711,169
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
PPM011216 PSS009307|
European Ancestry|
20,000 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): 0.0497 [0.0359, 0.0635] sex, age, birth date, deprivation index, 16 PCs —
PPM011217 PSS009081|
European Ancestry|
4,136 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): 0.0835 [0.0531, 0.1137] sex, age, birth date, deprivation index, 16 PCs —
PPM011218 PSS008635|
European Ancestry|
6,660 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): 0.0633 [0.0393, 0.0873] sex, age, birth date, deprivation index, 16 PCs —
PPM011219 PSS008409|
Greater Middle Eastern Ancestry|
1,200 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): 0.011 [-0.0461, 0.068] sex, age, birth date, deprivation index, 16 PCs —
PPM011220 PSS008189|
South Asian Ancestry|
6,331 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): 0.09 [0.0654, 0.1144] sex, age, birth date, deprivation index, 16 PCs —
PPM011222 PSS007754|
African Ancestry|
2,484 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): -0.0166 [-0.0561, 0.0229] sex, age, birth date, deprivation index, 16 PCs —
PPM011223 PSS008859|
African Ancestry|
3,924 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): 0.0213 [-0.0101, 0.0526] sex, age, birth date, deprivation index, 16 PCs —
PPM011221 PSS007972|
East Asian Ancestry|
1,810 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cataract — — Partial Correlation (partial-r): -0.0104 [-0.0567, 0.0359] 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
PSS007972 — — 1,810 individuals — East Asian China (East Asia) UKB —
PSS007754 — — 2,484 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008859 — — 3,924 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008409 — — 1,200 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009081 — — 4,136 individuals — European Poland (NE Europe) UKB —
PSS008635 — — 6,660 individuals — European Italy (South Europe) UKB —
PSS009307 — — 20,000 individuals — European UK (+ Ireland) UKB —
PSS008189 — — 6,331 individuals — South Asian India (South Asia) UKB —