PGS Preprint: PGP000052

Publication Information (EuropePMC)
Title Genomic risk scores for juvenile idiopathic arthritis and its subtypes
doi 10.1101/2020.02.20.20025924
Publication Date Feb. 23, 2020
Journal medRxiv Preprint
Author(s) Canovas R, Cobb J, Brozynska M, Bowes J, Li YR, Smith SL, Hakonarson H, Thomson W, Ellis J, Abraham G, Munro J, Inouye M.
Released in PGS: Feb. 27, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000114 GRS-JIA-20 PGP000052
Canovas R et al. medRxiv (2020)
Pre
Juvenile Idiopathic Arthritis juvenile idiopathic arthritis 26 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000114/ScoringFiles/PGS000114.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000261 PGS000114 (GRS-JIA-20) PSS000180 PGP000052
Canovas R et al. (2020)
Pre
Reported Trait: Juvenile Idiopathic Arthritis OR: 2.008[1.731, 2.345] AUROC: 0.671[0.635, 0.706]
PPM000260 PGS000114 (GRS-JIA-20) PSS000179 PGP000052
Canovas R et al. (2020)
Pre
Reported Trait: Juvenile Idiopathic Arthritis OR: 1.831[1.685, 1.991] AUROC: 0.657[0.631, 0.683]
PPM000263 PGS000114 (GRS-JIA-20) PSS000180 PGP000052
Canovas R et al. (2020)
Pre
Reported Trait: Juvenile Idiopathic Arthritis OR: 2.085[1.773, 2.471] AUROC: 0.738[0.705, 0.77] sex, genetic PCs 1-10
PPM000262 PGS000114 (GRS-JIA-20) PSS000179 PGP000052
Canovas R et al. (2020)
Pre
Reported Trait: Juvenile Idiopathic Arthritis OR: 1.838[1.686, 2.007] AUROC: 0.735[0.712, 0.758] sex, genetic PCs 1-10

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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