Polygenic Score (PGS) ID: PGS001313

Predicted Trait
Reported Trait Psoriasis (time-to-event)
Mapped Trait(s) psoriasis (EFO_0000676)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1159
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_HC1159
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 578
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
—
[
  • 7,688 cases
  • , 262,016 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
PPM009058 PSS004158|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriasis — AUROC: 0.69906 [0.60273, 0.7954] R²: 0.04185
Incremental AUROC (full-covars): 0.01899
PGS R2 (no covariates): 0.00732
PGS AUROC (no covariates): 0.62223 [0.54291, 0.70154]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009059 PSS004159|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriasis — AUROC: 0.72306 [0.61623, 0.82989] R²: 0.09162
Incremental AUROC (full-covars): 0.00222
PGS R2 (no covariates): 0.00378
PGS AUROC (no covariates): 0.48492 [0.37014, 0.5997]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009060 PSS004160|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriasis — AUROC: 0.66545 [0.64532, 0.68558] R²: 0.04468
Incremental AUROC (full-covars): 0.07449
PGS R2 (no covariates): 0.0337
PGS AUROC (no covariates): 0.64565 [0.62471, 0.66658]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009061 PSS004161|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriasis — AUROC: 0.63418 [0.59417, 0.67419] R²: 0.0236
Incremental AUROC (full-covars): 0.05154
PGS R2 (no covariates): 0.0123
PGS AUROC (no covariates): 0.60455 [0.56482, 0.64428]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009062 PSS004162|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriasis — AUROC: 0.67543 [0.66285, 0.68801] R²: 0.05117
Incremental AUROC (full-covars): 0.13853
PGS R2 (no covariates): 0.04966
PGS AUROC (no covariates): 0.6729 [0.66027, 0.68553]		 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
PSS004158 — —
[
  • 32 cases
  • , 6,465 controls
]
 — African unspecified — UKB —
PSS004159 — —
[
  • 22 cases
  • , 1,682 controls
]
 — East Asian — UKB —
PSS004160 — —
[
  • 723 cases
  • , 24,182 controls
]
 — European non-white British ancestry UKB —
PSS004161 — —
[
  • 186 cases
  • , 7,645 controls
]
 — South Asian — UKB —
PSS004162 — —
[
  • 1,956 cases
  • , 65,469 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)