Polygenic Score (PGS) ID: PGS001287

Predicted Trait
Reported Trait Psoriatic arthropathy
Mapped Trait(s) psoriatic arthritis (EFO_0003778)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC91
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_HC91
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 36
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
—
[
  • 829 cases
  • , 268,875 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
PPM008933 PSS004706|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriatic arthropathy — AUROC: 0.98006 [0.94602, 1.0] Incremental AUROC (full-covars): 0.00516
R²: 0.29301
PGS R2 (no covariates): 0.01017
PGS AUROC (no covariates): 0.72132 [0.63231, 0.81034]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008934 PSS004707|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriatic arthropathy — AUROC: 0.99354 [0.98059, 1.0] R²: 0.5357
Incremental AUROC (full-covars): -0.00088
PGS R2 (no covariates): 0.00227
PGS AUROC (no covariates): 0.47826 [0.0, 0.96911]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008935 PSS004708|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriatic arthropathy — AUROC: 0.72814 [0.67154, 0.78475] R²: 0.05154
Incremental AUROC (full-covars): 0.08346
PGS R2 (no covariates): 0.0335
PGS AUROC (no covariates): 0.67648 [0.61155, 0.7414]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008936 PSS004709|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriatic arthropathy — AUROC: 0.71827 [0.61363, 0.82292] R²: 0.04395
Incremental AUROC (full-covars): 0.00838
PGS R2 (no covariates): 0.00229
PGS AUROC (no covariates): 0.56943 [0.44876, 0.69011]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008937 PSS004710|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriatic arthropathy — AUROC: 0.6376 [0.60073, 0.67447] R²: 0.02161
Incremental AUROC (full-covars): 0.0945
PGS R2 (no covariates): 0.02111
PGS AUROC (no covariates): 0.63567 [0.598, 0.67334]		 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
PSS004706 — —
[
  • 2 cases
  • , 6,495 controls
]
 — African unspecified — UKB —
PSS004707 — —
[
  • 2 cases
  • , 1,702 controls
]
 — East Asian — UKB —
PSS004708 — —
[
  • 81 cases
  • , 24,824 controls
]
 — European non-white British ancestry UKB —
PSS004709 — —
[
  • 21 cases
  • , 7,810 controls
]
 — South Asian — UKB —
PSS004710 — —
[
  • 231 cases
  • , 67,194 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)