Polygenic Score (PGS) ID: PGS001312

Predicted Trait
Reported Trait Psoriasis
Mapped Trait(s) psoriasis (EFO_0000676)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC38
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_HC38
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 204
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
—
[
  • 4,439 cases
  • , 265,265 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
PPM009053 PSS004471|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriasis — AUROC: 0.73107 [0.60624, 0.85591] R²: 0.06593
Incremental AUROC (full-covars): 0.0282
PGS R2 (no covariates): 0.01927
PGS AUROC (no covariates): 0.62557 [0.48848, 0.76266]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009054 PSS004472|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriasis — AUROC: 0.88867 [0.80531, 0.97202] R²: 0.24575
Incremental AUROC (full-covars): 0.01187
PGS R2 (no covariates): 0.00399
PGS AUROC (no covariates): 0.57774 [0.40533, 0.75016]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009055 PSS004473|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriasis — AUROC: 0.68424 [0.65757, 0.71091] R²: 0.05057
Incremental AUROC (full-covars): 0.0981
PGS R2 (no covariates): 0.04137
PGS AUROC (no covariates): 0.66409 [0.63596, 0.69222]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009056 PSS004474|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriasis — AUROC: 0.6849 [0.63397, 0.73584] R²: 0.0448
Incremental AUROC (full-covars): 0.052
PGS R2 (no covariates): 0.02087
PGS AUROC (no covariates): 0.64825 [0.59861, 0.6979]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009057 PSS004475|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Psoriasis — AUROC: 0.69754 [0.68165, 0.71343] R²: 0.05574
Incremental AUROC (full-covars): 0.14505
PGS R2 (no covariates): 0.05226
PGS AUROC (no covariates): 0.69158 [0.6754, 0.70775]		 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
PSS004471 — —
[
  • 19 cases
  • , 6,478 controls
]
 — African unspecified — UKB —
PSS004472 — —
[
  • 10 cases
  • , 1,694 controls
]
 — East Asian — UKB —
PSS004473 — —
[
  • 416 cases
  • , 24,489 controls
]
 — European non-white British ancestry UKB —
PSS004474 — —
[
  • 108 cases
  • , 7,723 controls
]
 — South Asian — UKB —
PSS004475 — —
[
  • 1,146 cases
  • , 66,279 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)