Polygenic Score (PGS) ID: PGS000941

Predicted Trait
Reported Trait Iridocyclitis (time-to-event)
Mapped Trait(s) Iridocyclitis (HP_0001094)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC868
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_HC868
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 1,412 cases
  • , 268,292 controls
]
 European UKB — — — white British ancestry —

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
PPM007531 PSS004667|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE iridocyclitis — AUROC: 0.68898 [0.62053, 0.75743] PGS R2 (no covariates): 0.00183
Incremental AUROC (full-covars): 0.00666
R²: 0.04292
PGS AUROC (no covariates): 0.50378 [0.48811, 0.51944]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007532 PSS004668|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE iridocyclitis — AUROC: 0.8465 [0.65581, 1.0] R²: 0.16291
Incremental AUROC (full-covars): -0.00024
PGS R2 (no covariates): 0.00141
PGS AUROC (no covariates): 0.49529 [0.49299, 0.49759]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007533 PSS004669|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE iridocyclitis — AUROC: 0.67429 [0.6184, 0.73017] R²: 0.04715
Incremental AUROC (full-covars): 0.08652
PGS R2 (no covariates): 0.04197
PGS AUROC (no covariates): 0.62279 [0.57834, 0.66724]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007534 PSS004670|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE iridocyclitis — AUROC: 0.67356 [0.61463, 0.73249] R²: 0.03247
Incremental AUROC (full-covars): -0.00127
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49832 [0.48312, 0.51352]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007535 PSS004671|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE iridocyclitis — AUROC: 0.66117 [0.62955, 0.69278] R²: 0.0447
Incremental AUROC (full-covars): 0.10569
PGS R2 (no covariates): 0.04482
PGS AUROC (no covariates): 0.63375 [0.60929, 0.65822]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004668 — —
[
  • 5 cases
  • , 1,699 controls
]
 — East Asian — UKB —
PSS004669 — —
[
  • 106 cases
  • , 24,799 controls
]
 — European non-white British ancestry UKB —
PSS004670 — —
[
  • 65 cases
  • , 7,766 controls
]
 — South Asian — UKB —
PSS004671 — —
[
  • 367 cases
  • , 67,058 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004667 — —
[
  • 63 cases
  • , 6,434 controls
]
 — African unspecified — UKB —