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
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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
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
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