Trait: psoriatic arthritis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003778
Description Joint inflammation associated with psoriasis. [NCIT: P378]
Trait category
Immune system disorder
Synonyms 12 synonyms
  • Arthritic Psoriasis
  • Arthritis, Psoriatic
  • PsA
  • Psoriasis Arthropathica
  • Psoriasis, Arthritic
  • arthritis psoriatica
  • arthropathic psoriasis
  • psoriatic arthritis
  • psoriatic arthritis, susceptibility to
  • psoriatic arthritis, susceptibility to, 1
  • psoriatic arthropathy
  • susceptibility to psoriatic arthritis
Mapped terms 16 mapped terms
  • DOID:9008
  • ICD10:M07
  • ICD9:696.0
  • MEDGEN:2077
  • MESH:D015535
  • MONDO:0011849
  • MeSH:D015535
  • MedDRA:10037160
  • NANDO:2201059
  • NCIT:C61277
  • NCIt:C61277
  • OMIM:607507
  • Orphanet:40050
  • SCTID:156370009
  • UMLS:C0003872
  • icd11.foundation:868183264

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000198
(G-PROB_PsA)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Psoriatic arthritis psoriatic arthritis 31
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000198/ScoringFiles/PGS000198.txt.gz
PGS000342
(wGRS_PsA)
 PGP000111 |
Smith MP et al. J Psoriasis Psoriatic Arthritis (2020)
 Psoriatic arthritis psoriatic arthritis 11
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000342/ScoringFiles/PGS000342.txt.gz
PGS000343
(wGRS_PsA_HLA)
 PGP000111 |
Smith MP et al. J Psoriasis Psoriatic Arthritis (2020)
 Psoriatic arthritis psoriatic arthritis 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000343/ScoringFiles/PGS000343.txt.gz
PGS001287
(GBE_HC91)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Psoriatic arthropathy psoriatic arthritis 36
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001287/ScoringFiles/PGS001287.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
PPM000581 PGS000198
(G-PROB_PsA)
 PSS000313|
European Ancestry|
243 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Reported Trait: Psoriatic arthritis diagnosis in patient with arthritis — AUROC: 0.62 [0.48, 0.8] — — (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000575 PGS000198
(G-PROB_PsA)
 PSS000312|
European Ancestry|
245 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Reported Trait: Psoriatic arthritis diagnosis in patient with arthritis — AUROC: 0.71 [0.63, 0.82] — — (Setting II: Assigning patient diagnoses based on medical records)
PPM000569 PGS000198
(G-PROB_PsA)
 PSS000321|
Multi-ancestry (including European)|
1,211 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Reported Trait: Psoriatic arthritis diagnosis in patient with arthritis — AUROC: 0.61 [0.52, 0.69] — — (Setting I: Assigning patient diagnoses based on billing codes)
PPM000971 PGS000342
(wGRS_PsA)
 PSS000490|
Ancestry Not Reported|
543 individuals
 PGP000111 |
Smith MP et al. J Psoriasis Psoriatic Arthritis (2020)
 Reported Trait: Psoriatic arthritis — AUROC: 0.562 [0.506, 0.618] — — —
PPM000972 PGS000343
(wGRS_PsA_HLA)
 PSS000490|
Ancestry Not Reported|
543 individuals
 PGP000111 |
Smith MP et al. J Psoriasis Psoriatic Arthritis (2020)
 Reported Trait: Psoriatic arthritis — AUROC: 0.569 [0.513, 0.625] — — —
PPM008933 PGS001287
(GBE_HC91)
 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 PGS001287
(GBE_HC91)
 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 PGS001287
(GBE_HC91)
 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 PGS001287
(GBE_HC91)
 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 PGS001287
(GBE_HC91)
 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 —
PSS000312 Setting II: Based on ICD codes and review of medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 8.0 years
[
  • 30 cases
  • , 215 controls
]
,
32.0 % Male samples
 — European — PHB —
PSS000313 Setting III: Based on ICD codes and final diagnosis in medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 7.0 years
[
  • 22 cases
  • , 221 controls
]
,
32.0 % Male samples
 — European — PHB —
PSS004709 — —
[
  • 21 cases
  • , 7,810 controls
]
 — South Asian — UKB —
PSS004710 — —
[
  • 231 cases
  • , 67,194 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS000490 Cases included physician-confirmed psoriatic arthritis (PsA). Controls inclded individuals with psoriasis with no history of joint symptoms (psoriasis only - PsO). —
[
  • 140 cases
  • , 403 controls
]
 — NR — NR —
PSS000321 Setting I: Based on ICD codes and expert opinion (ACR2010 criteria), in eMERGE network EMR database from Stanaway 2018; controls = other non-matching arthritis diseases Median = 16.0 years
[
  • 52 cases
  • , 1,159 controls
]
,
43.0 % Male samples
 — European, African unspecified, Asian unspecified, NR Primarily European, African and Asian ancestry eMERGE —