Trait: Arthropathy

Trait Information
Identifier HP_0003040
Trait category
Other trait
Synonym Disease of the joints
Mapped terms 3 mapped terms
  • MSH:D007592
  • SNOMEDCT_US:399269003
  • UMLS:C0022408

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)
PGS001522
(GBE_HC1213)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Psoriatic and enteropathic arthropathies (time-to-event) Arthropathy 17
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001522/ScoringFiles/PGS001522.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
PPM005220 PGS001522
(GBE_HC1213)
PSS004198|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriatic and enteropathic arthropathies AUROC: 0.98137 [0.94929, 1.0] : 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 PGS001522
(GBE_HC1213)
PSS004199|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriatic and enteropathic arthropathies AUROC: 0.9318 [0.86946, 0.99415] : 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 PGS001522
(GBE_HC1213)
PSS004200|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriatic and enteropathic arthropathies AUROC: 0.68946 [0.62601, 0.75291] : 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 PGS001522
(GBE_HC1213)
PSS004201|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriatic and enteropathic arthropathies AUROC: 0.78586 [0.68309, 0.88863] : 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 PGS001522
(GBE_HC1213)
PSS004202|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE psoriatic and enteropathic arthropathies AUROC: 0.58666 [0.54165, 0.63166] : 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)