Trait: psoriasis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000676
Description An autoimmune condition characterized by red, well-delineated plaques with silvery scales that are usually on the extensor surfaces and scalp. They can occasionally present with these manifestations: pustules; erythema and scaling in intertriginous areas, and erythroderma, that are often distributed on extensor surfaces and scalp. [NCIT: P378]
Trait category
Immune system disorder
Synonyms 20 synonyms
  • OTHER PSORIASIS
  • Other and unspecified pityriasis
  • Other psoriasis and similar disorders
  • Other psoriasis and similar disorders (disorder)
  • Other psoriasis and similar disorders excluding psoriatic arthropathy
  • PITYRIASIS NEC & NOS
  • PSORIAS RELATED DIS NEC
  • PUSTULAR PSORIASIS OF PALMS SOLES
  • PUSTULOSIS OF PALMS SOLES
  • Palmoplantaris Pustulosis
  • Psoriases
  • Psoriasis and similar disorders
  • Psoriasis and similar disorders (disorder)
  • Psoriasis and similar disorders (navigational concept)
  • Psoriasis and similar disorders NOS
  • Psoriasis and similar disorders NOS (disorder)
  • Pustular Psoriasis of Palms and Soles
  • Pustulosis Palmaris et Plantaris
  • Pustulosis of Palms and Soles
  • psoriasis
Mapped terms 23 mapped terms
  • DOID:8893
  • GARD:0010262
  • ICD10:L40
  • ICD10:L40.9
  • ICD9:696
  • ICD9:696.1
  • ICD9:696.5
  • ICD9:696.8
  • MESH:D011565
  • MONDO:0005083
  • MeSH:D011565
  • MedDRA:10037153
  • NCIT:C3346
  • NCIt:C3346
  • OMIM:177900
  • OMIM:602723
  • OMIM:605606
  • OMIM:612599
  • OMIM:614070
  • OMIMPS:177900
  • SCTID:9014002
  • SNOMEDCT:9014002
  • UMLS:C0033860

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001312
(GBE_HC38)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Psoriasis psoriasis 204
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001312/ScoringFiles/PGS001312.txt.gz
PGS001313
(GBE_HC1159)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Psoriasis (time-to-event) psoriasis 578
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001313/ScoringFiles/PGS001313.txt.gz

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)
Evaluated Score 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
PPM009062 PGS001313
(GBE_HC1159)
PSS004162|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriasis AUROC: 0.67543 [0.66285, 0.68801] : 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
PPM009061 PGS001313
(GBE_HC1159)
PSS004161|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriasis AUROC: 0.63418 [0.59417, 0.67419] : 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
PPM009060 PGS001313
(GBE_HC1159)
PSS004160|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriasis AUROC: 0.66545 [0.64532, 0.68558] : 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
PPM009059 PGS001313
(GBE_HC1159)
PSS004159|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriasis AUROC: 0.72306 [0.61623, 0.82989] : 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
PPM009058 PGS001313
(GBE_HC1159)
PSS004158|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriasis AUROC: 0.69906 [0.60273, 0.7954] : 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
PPM009057 PGS001312
(GBE_HC38)
PSS004475|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Psoriasis AUROC: 0.69754 [0.68165, 0.71343] : 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
PPM009056 PGS001312
(GBE_HC38)
PSS004474|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Psoriasis AUROC: 0.6849 [0.63397, 0.73584] : 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
PPM009055 PGS001312
(GBE_HC38)
PSS004473|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Psoriasis AUROC: 0.68424 [0.65757, 0.71091] : 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
PPM009054 PGS001312
(GBE_HC38)
PSS004472|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Psoriasis AUROC: 0.88867 [0.80531, 0.97202] : 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
PPM009053 PGS001312
(GBE_HC38)
PSS004471|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Psoriasis AUROC: 0.73107 [0.60624, 0.85591] : 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

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)
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)