Polygenic Score (PGS) ID: PGS002043

Predicted Trait
Reported Trait Glaucoma
Mapped Trait(s) glaucoma (EFO_0000516)
Additional Trait Information sense organs
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_365
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 672,952
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
PPM011208 PSS009306|
European Ancestry|
19,592 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0458 [0.0318, 0.0598] sex, age, birth date, deprivation index, 16 PCs
PPM011209 PSS009080|
European Ancestry|
4,066 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0458 [0.015, 0.0765] sex, age, birth date, deprivation index, 16 PCs
PPM011211 PSS008408|
Greater Middle Eastern Ancestry|
1,181 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0637 [0.0062, 0.1208] sex, age, birth date, deprivation index, 16 PCs
PPM011212 PSS008188|
South Asian Ancestry|
6,176 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0216 [-0.0034, 0.0465] sex, age, birth date, deprivation index, 16 PCs
PPM011213 PSS007971|
East Asian Ancestry|
1,783 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0214 [-0.0253, 0.068] sex, age, birth date, deprivation index, 16 PCs
PPM011214 PSS007753|
African Ancestry|
2,447 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0126 [-0.0272, 0.0524] sex, age, birth date, deprivation index, 16 PCs
PPM011215 PSS008858|
African Ancestry|
3,854 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0279 [-0.0037, 0.0595] sex, age, birth date, deprivation index, 16 PCs
PPM011210 PSS008634|
European Ancestry|
6,540 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glaucoma Partial Correlation (partial-r): 0.0366 [0.0123, 0.0608] 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
PSS007753 2,447 individuals African American or Afro-Caribbean Carribean UKB
PSS009080 4,066 individuals European Poland (NE Europe) UKB
PSS008408 1,181 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009306 19,592 individuals European UK (+ Ireland) UKB
PSS008858 3,854 individuals African unspecified Nigeria (West Africa) UKB
PSS008188 6,176 individuals South Asian India (South Asia) UKB
PSS008634 6,540 individuals European Italy (South Europe) UKB
PSS007971 1,783 individuals East Asian China (East Asia) UKB