Trait: reactive arthritis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007460
Description Reactive arthritis (ReA) is an autoimmune disorder belonging to the group of seronegative spondyloarthropathies and is characterized by the classic triad of arthritis, urethritis and conjunctivitis. [Orphanet: 29207]
Trait category
Immune system disorder
Synonyms 19 synonyms
  • Arthritis, Reactive
  • Fiessinger Leroy Reiter syndrome
  • Fiessinger-Leroy disease
  • Fiessinger-Leroy-Reiter syndrome
  • PIRA
  • Post-bacterial arthropathy
  • Reactive arthritis
  • Reiter disease
  • Reiter syndrome
  • Reiter's disease
  • Reiter's syndrome
  • arthritis urethritica
  • polyarthritis enterica
  • post-bacterial arthropathy
  • post-infectious arthritis
  • post-infectious reactive arthropathy
  • postdysenteric arthropathy
  • reactive arthritis
  • venereal arthritis
Mapped terms 19 mapped terms
  • DOID:6196
  • GARD:5693
  • ICD10:M03
  • ICD9:099.3
  • ICD9:711.3
  • ICD9:711.30
  • ICD9:711.40
  • MEDGEN:39047
  • MESH:D016918
  • MONDO:0017376
  • MeSH:D016918
  • MedDRA:10003267
  • MedDRA:10037994
  • MedDRA:10038294
  • NCIT:C128332
  • NORD:1650
  • Orphanet:29207
  • SCTID:129133005
  • UMLS:C0085435

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)
PGS001110
(GBE_HC1209)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reactive arthropathies (time-to-event) reactive arthritis 6
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001110/ScoringFiles/PGS001110.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
PPM008289 PGS001110
(GBE_HC1209)
 PSS004183|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE reactive arthropathies — AUROC: 0.9594 [0.92062, 0.99818] R²: 0.17918
Incremental AUROC (full-covars): 0.00395
PGS R2 (no covariates): 0.00991
PGS AUROC (no covariates): 0.72061 [0.49213, 0.9491]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008290 PGS001110
(GBE_HC1209)
 PSS004185|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE reactive arthropathies — AUROC: 0.77096 [0.63921, 0.90271] R²: 0.09743
Incremental AUROC (full-covars): 0.03274
PGS R2 (no covariates): 0.03411
PGS AUROC (no covariates): 0.65137 [0.47674, 0.826]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008291 PGS001110
(GBE_HC1209)
 PSS004186|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE reactive arthropathies — AUROC: 0.94552 [0.83969, 1.0] R²: 0.25627
Incremental AUROC (full-covars): 0.00045
PGS R2 (no covariates): 0.00071
PGS AUROC (no covariates): 0.67786 [0.66768, 0.68805]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008292 PGS001110
(GBE_HC1209)
 PSS004187|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE reactive arthropathies — AUROC: 0.6839 [0.58647, 0.78132] R²: 0.03053
Incremental AUROC (full-covars): 0.07922
PGS R2 (no covariates): 0.02879
PGS AUROC (no covariates): 0.66167 [0.54859, 0.77475]		 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
PSS004183 — —
[
  • 3 cases
  • , 6,494 controls
]
 — African unspecified — UKB —
PSS004185 — —
[
  • 12 cases
  • , 24,893 controls
]
 — European non-white British ancestry UKB —
PSS004186 — —
[
  • 2 cases
  • , 7,829 controls
]
 — South Asian — UKB —
PSS004187 — —
[
  • 30 cases
  • , 67,395 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)