Polygenic Score (PGS) ID: PGS002045

Predicted Trait
Reported Trait Inflammation of the eye
Mapped Trait(s)
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_371
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 527,030
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
PPM011225 PSS009082|
European Ancestry|
4,069 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): -0.007 [-0.0378, 0.0238] sex, age, birth date, deprivation index, 16 PCs —
PPM011227 PSS008410|
Greater Middle Eastern Ancestry|
1,183 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): 0.0226 [-0.0349, 0.08] sex, age, birth date, deprivation index, 16 PCs —
PPM011228 PSS008190|
South Asian Ancestry|
6,184 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): 0.01 [-0.015, 0.0349] sex, age, birth date, deprivation index, 16 PCs —
PPM011229 PSS007973|
East Asian Ancestry|
1,779 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): -0.0042 [-0.0509, 0.0426] sex, age, birth date, deprivation index, 16 PCs —
PPM011230 PSS007755|
African Ancestry|
2,428 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): -0.0067 [-0.0466, 0.0333] sex, age, birth date, deprivation index, 16 PCs —
PPM011231 PSS008860|
African Ancestry|
3,820 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): -0.008 [-0.0397, 0.0238] sex, age, birth date, deprivation index, 16 PCs —
PPM011224 PSS009308|
European Ancestry|
19,618 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): 0.0162 [0.0022, 0.0302] sex, age, birth date, deprivation index, 16 PCs —
PPM011226 PSS008636|
European Ancestry|
6,561 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Inflammation of the eye — — Partial Correlation (partial-r): 0.0309 [0.0067, 0.0551] 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
PSS007973 — — 1,779 individuals — East Asian China (East Asia) UKB —
PSS007755 — — 2,428 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008636 — — 6,561 individuals — European Italy (South Europe) UKB —
PSS009082 — — 4,069 individuals — European Poland (NE Europe) UKB —
PSS008410 — — 1,183 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008860 — — 3,820 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008190 — — 6,184 individuals — South Asian India (South Asia) UKB —
PSS009308 — — 19,618 individuals — European UK (+ Ireland) UKB —