PGS Publication: PGP000052

Publication Information (EuropePMC)
Title Genomic risk scores for juvenile idiopathic arthritis and its subtypes.
PubMed ID 32887683(Europe PMC)
doi 10.1136/annrheumdis-2020-217421
Publication Date Sept. 4, 2020
Journal Ann Rheum Dis
Author(s) Cánovas R, Cobb J, Brozynska M, Bowes J, Li YR, Smith SL, Hakonarson H, Thomson W, Ellis JA, Abraham G, Munro JE, Inouye M.
Released in PGS Catalog: Feb. 27, 2020

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

PGS Developed By This Publication

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)
PGS000324
(GRS-JIA-ERA-20)
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Enthesitis-related Juvenile Idiophatic Arthritis enthesitis-related juvenile idiopathic arthritis 138
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000324/ScoringFiles/PGS000324.txt.gz
PGS000326
(GRS-JIA-RFN-20)
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Rheumatoid-factor-negative Polyarthritis (Juvenile Idiophatic Arthritis) polyarticular juvenile idiopathic arthritis, rheumatoid factor negative 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000326/ScoringFiles/PGS000326.txt.gz
PGS000114
(GRS-JIA-20)
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Juvenile Idiopathic Arthritis juvenile idiopathic arthritis 26
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000114/ScoringFiles/PGS000114.txt.gz
PGS000325
(GRS-JIA-Oli-20)
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Oligoarthritis Juvenile Idiophatic Arthritis oligoarticular juvenile idiopathic arthritis 21
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000325/ScoringFiles/PGS000325.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
PPM000878 PGS000326
(GRS-JIA-RFN-20)
 PSS000434|
European Ancestry|
653 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Rheumatoid-factor-negative Polyarthritis OR: 1.71 [1.42, 2.07] AUROC: 0.74 [0.68, 0.8] — sex, genetic PCs 1-10 —
PPM000872 PGS000326
(GRS-JIA-RFN-20)
 PSS000434|
European Ancestry|
653 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Rheumatoid-factor-negative Polyarthritis OR: 1.69 [1.42, 2.02] AUROC: 0.66 [0.59, 0.73] — — —
PPM000262 PGS000114
(GRS-JIA-20)
 PSS000179|
European Ancestry|
3,513 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Juvenile Idiopathic Arthritis OR: 1.838 [1.686, 2.007] AUROC: 0.735 [0.712, 0.758] — sex, genetic PCs 1-10 —
PPM000263 PGS000114
(GRS-JIA-20)
 PSS000180|
European Ancestry|
940 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Juvenile Idiopathic Arthritis OR: 2.085 [1.773, 2.471] AUROC: 0.738 [0.705, 0.77] — sex, genetic PCs 1-10 —
PPM000260 PGS000114
(GRS-JIA-20)
 PSS000179|
European Ancestry|
3,513 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Juvenile Idiopathic Arthritis OR: 1.831 [1.685, 1.991] AUROC: 0.657 [0.631, 0.683] — — —
PPM000261 PGS000114
(GRS-JIA-20)
 PSS000180|
European Ancestry|
940 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Juvenile Idiopathic Arthritis OR: 2.008 [1.731, 2.345] AUROC: 0.671 [0.635, 0.706] — — —
PPM000874 PGS000324
(GRS-JIA-ERA-20)
 PSS000432|
European Ancestry|
594 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Enthesitis-related Arthritis OR: 3.09 [2.07, 5.04] AUROC: 0.93 [0.86, 0.99] — sex, genetic PCs 1-10 —
PPM000875 PGS000325
(GRS-JIA-Oli-20)
 PSS000430|
European Ancestry|
3,157 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Oligoarthritis Juvenile Idiophatic Arthritis OR: 1.93 [1.75, 2.13] AUROC: 0.8 [0.77, 0.84] — sex, genetic PCs 1-10 —
PPM000876 PGS000325
(GRS-JIA-Oli-20)
 PSS000433|
European Ancestry|
737 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Oligoarthritis Juvenile Idiophatic Arthritis OR: 2.19 [1.81, 2.71] AUROC: 0.79 [0.76, 0.83] — sex, genetic PCs 1-10 —
PPM000877 PGS000326
(GRS-JIA-RFN-20)
 PSS000431|
European Ancestry|
3,089 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Rheumatoid-factor-negative Polyarthritis OR: 1.51 [1.35, 1.68] AUROC: 0.76 [0.72, 0.8] — sex, genetic PCs 1-10 —
PPM000873 PGS000324
(GRS-JIA-ERA-20)
 PSS000429|
European Ancestry|
3,020 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Enthesitis-related Arthritis OR: 1.86 [1.61, 2.14] AUROC: 0.75 [0.68, 0.82] — sex, genetic PCs 1-10 —
PPM000867 PGS000324
(GRS-JIA-ERA-20)
 PSS000429|
European Ancestry|
3,020 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Enthesitis-related Arthritis OR: 1.84 [1.6, 2.17] AUROC: 0.7 [0.63, 0.77] — — —
PPM000868 PGS000324
(GRS-JIA-ERA-20)
 PSS000432|
European Ancestry|
594 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Enthesitis-related Arthritis OR: 2.99 [2.11, 4.54] AUROC: 0.84 [0.71, 0.97] — — —
PPM000869 PGS000325
(GRS-JIA-Oli-20)
 PSS000430|
European Ancestry|
3,157 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Oligoarthritis Juvenile Idiophatic Arthritis OR: 1.93 [1.76, 2.11] AUROC: 0.77 [0.73, 0.8] — — —
PPM000870 PGS000325
(GRS-JIA-Oli-20)
 PSS000433|
European Ancestry|
737 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Oligoarthritis Juvenile Idiophatic Arthritis OR: 2.24 [1.88, 2.71] AUROC: 0.74 [0.7, 0.79] — — —
PPM000871 PGS000326
(GRS-JIA-RFN-20)
 PSS000431|
European Ancestry|
3,089 individuals
 PGP000052 |
Cánovas R et al. Ann Rheum Dis (2020)
 Reported Trait: Rheumatoid-factor-negative Polyarthritis OR: 1.48 [1.33, 1.64] AUROC: 0.64 [0.59, 0.69] — — —

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
PSS000179 JIA diagnosis was made according to International League of Associations for Rheumatology standards (PMID:14760812) from EHR. Control subjects were unrelated and disease-free children. —
[
  • 559 cases
  • , 2,954 controls
]
,
47.5 % Male samples
 — European — CHOP —
PSS000180 Diagnosis of JIA by a paediatric rheumatologist. —
[
  • 362 cases
  • , 578 controls
]
,
48.9 % Male samples
 — European — CLARITY Cohort description (PMID): 23153063
PSS000429 JIA diagnosis was made according to International League of Associations for Rheumatology standards (PMID:14760812) from EHR. Control subjects were unrelated and disease-free children. —
[
  • 66 cases
  • , 2,954 controls
]
,
51.46 % Male samples
 — European — CHOP —
PSS000430 JIA diagnosis was made according to International League of Associations for Rheumatology standards (PMID:14760812) from EHR. Control subjects were unrelated and disease-free children. —
[
  • 203 cases
  • , 2,954 controls
]
,
49.19 % Male samples
 — European — CHOP —
PSS000431 JIA diagnosis was made according to International League of Associations for Rheumatology standards (PMID:14760812) from EHR. Control subjects were unrelated and disease-free children. —
[
  • 135 cases
  • , 2,954 controls
]
,
50.11 % Male samples
 — European — CHOP —
PSS000432 Diagnosis of JIA by a paediatric rheumatologist. —
[
  • 16 cases
  • , 578 controls
]
,
58.59 % Male samples
 — European — CLARITY Cohort description (PMID): 23153063
PSS000433 Diagnosis of JIA by a paediatric rheumatologist. —
[
  • 159 cases
  • , 578 controls
]
,
51.15 % Male samples
 — European — CLARITY Cohort description (PMID): 23153063
PSS000434 Diagnosis of JIA by a paediatric rheumatologist. —
[
  • 75 cases
  • , 578 controls
]
,
54.82 % Male samples
 — European — CLARITY Cohort description (PMID): 23153063