Trait: Arthropathy

Trait Information
Identifier HP_0003040
Trait category
Other trait
Synonym Disease of the joints
Mapped terms 2 mapped terms
  • 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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001522
(GBE_HC1213)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Psoriatic and enteropathic arthropathies (time-to-event) Arthropathy 17
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001522/ScoringFiles/PGS001522.txt.gz
PGS001877
(portability-PLR_716)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Other arthropathies Arthropathy 17,363
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001877/ScoringFiles/PGS001877.txt.gz
PGS002090
(portability-ldpred2_716)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Other arthropathies Arthropathy 859,336
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002090/ScoringFiles/PGS002090.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. 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 PGS001522
(GBE_HC1213)
 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 PGS001522
(GBE_HC1213)
 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 PGS001522
(GBE_HC1213)
 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 PGS001522
(GBE_HC1213)
 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
PPM009901 PGS001877
(portability-PLR_716)
 PSS009354|
European Ancestry|
19,847 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0461 [0.0322, 0.0599] sex, age, birth date, deprivation index, 16 PCs —
PPM009902 PGS001877
(portability-PLR_716)
 PSS009128|
European Ancestry|
4,104 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0184 [-0.0122, 0.0491] sex, age, birth date, deprivation index, 16 PCs —
PPM009903 PGS001877
(portability-PLR_716)
 PSS008682|
European Ancestry|
6,617 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.045 [0.0209, 0.0691] sex, age, birth date, deprivation index, 16 PCs —
PPM009904 PGS001877
(portability-PLR_716)
 PSS008456|
Greater Middle Eastern Ancestry|
1,195 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0341 [-0.0232, 0.0911] sex, age, birth date, deprivation index, 16 PCs —
PPM009905 PGS001877
(portability-PLR_716)
 PSS008236|
South Asian Ancestry|
6,278 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0386 [0.0138, 0.0633] sex, age, birth date, deprivation index, 16 PCs —
PPM009906 PGS001877
(portability-PLR_716)
 PSS008015|
East Asian Ancestry|
1,805 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): -0.0084 [-0.0547, 0.038] sex, age, birth date, deprivation index, 16 PCs —
PPM009907 PGS001877
(portability-PLR_716)
 PSS007800|
African Ancestry|
2,465 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): -0.0304 [-0.07, 0.0092] sex, age, birth date, deprivation index, 16 PCs —
PPM009908 PGS001877
(portability-PLR_716)
 PSS008904|
African Ancestry|
3,893 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0315 [0.0, 0.0629] sex, age, birth date, deprivation index, 16 PCs —
PPM011577 PGS002090
(portability-ldpred2_716)
 PSS009354|
European Ancestry|
19,847 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0698 [0.0559, 0.0836] sex, age, birth date, deprivation index, 16 PCs —
PPM011578 PGS002090
(portability-ldpred2_716)
 PSS009128|
European Ancestry|
4,104 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0524 [0.0217, 0.0829] sex, age, birth date, deprivation index, 16 PCs —
PPM011579 PGS002090
(portability-ldpred2_716)
 PSS008682|
European Ancestry|
6,617 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0702 [0.0462, 0.0942] sex, age, birth date, deprivation index, 16 PCs —
PPM011580 PGS002090
(portability-ldpred2_716)
 PSS008456|
Greater Middle Eastern Ancestry|
1,195 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0373 [-0.0199, 0.0943] sex, age, birth date, deprivation index, 16 PCs —
PPM011582 PGS002090
(portability-ldpred2_716)
 PSS008015|
East Asian Ancestry|
1,805 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): -0.0166 [-0.0629, 0.0298] sex, age, birth date, deprivation index, 16 PCs —
PPM011583 PGS002090
(portability-ldpred2_716)
 PSS007800|
African Ancestry|
2,465 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0175 [-0.0221, 0.0571] sex, age, birth date, deprivation index, 16 PCs —
PPM011584 PGS002090
(portability-ldpred2_716)
 PSS008904|
African Ancestry|
3,893 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0202 [-0.0113, 0.0517] sex, age, birth date, deprivation index, 16 PCs —
PPM011581 PGS002090
(portability-ldpred2_716)
 PSS008236|
South Asian Ancestry|
6,278 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0588 [0.0341, 0.0834] sex, age, birth date, deprivation index, 16 PCs —

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
PSS009128 — — 4,104 individuals — European Poland (NE Europe) UKB —
PSS008456 — — 1,195 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009354 — — 19,847 individuals — European UK (+ Ireland) UKB —
PSS008682 — — 6,617 individuals — European Italy (South Europe) UKB —
PSS008236 — — 6,278 individuals — South Asian India (South Asia) UKB —
PSS008904 — — 3,893 individuals — African unspecified Nigeria (West Africa) UKB —
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)
PSS008015 — — 1,805 individuals — East Asian China (East Asia) UKB —
PSS007800 — — 2,465 individuals — African American or Afro-Caribbean Carribean UKB —