Polygenic Score (PGS) ID: PGS001522

Predicted Trait
Reported Trait Psoriatic and enteropathic arthropathies (time-to-event)
Mapped Trait(s) Arthropathy (HP_0003040)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1213
Released in PGS Catalog: Nov. 25, 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_HC1213
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 17
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
—
[
  • 555 cases
  • , 269,149 controls
]
 European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005220 PSS004198|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriatic and enteropathic arthropathies — AUROC: 0.98137 [0.94929, 1.0] R²: 0.29775
Incremental AUROC (full-covars): 0.00647
PGS R2 (no covariates): 0.02434
PGS AUROC (no covariates): 0.77983 [0.65036, 0.9093]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005221 PSS004199|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriatic and enteropathic arthropathies — AUROC: 0.9318 [0.86946, 0.99415] R²: 0.20976
Incremental AUROC (full-covars): 0.03273
PGS R2 (no covariates): 0.06659
PGS AUROC (no covariates): 0.67274 [0.26001, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005222 PSS004200|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriatic and enteropathic arthropathies — AUROC: 0.68946 [0.62601, 0.75291] R²: 0.03139
Incremental AUROC (full-covars): 0.05789
PGS R2 (no covariates): 0.01065
PGS AUROC (no covariates): 0.60522 [0.52232, 0.68812]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005223 PSS004201|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriatic and enteropathic arthropathies — AUROC: 0.78586 [0.68309, 0.88863] R²: 0.08779
Incremental AUROC (full-covars): -0.01064
PGS R2 (no covariates): 0.00177
PGS AUROC (no covariates): 0.56306 [0.42254, 0.70358]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005224 PSS004202|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE psoriatic and enteropathic arthropathies — AUROC: 0.58666 [0.54165, 0.63166] R²: 0.00849
Incremental AUROC (full-covars): 0.04415
PGS R2 (no covariates): 0.00801
PGS AUROC (no covariates): 0.57558 [0.52895, 0.62221]		 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
PSS004198 — —
[
  • 2 cases
  • , 6,495 controls
]
 — African unspecified — UKB —
PSS004199 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004200 — —
[
  • 56 cases
  • , 24,849 controls
]
 — European non-white British ancestry UKB —
PSS004201 — —
[
  • 16 cases
  • , 7,815 controls
]
 — South Asian — UKB —
PSS004202 — —
[
  • 163 cases
  • , 67,262 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)