Polygenic Score (PGS) ID: PGS000114

Predicted Trait
Reported Trait Juvenile Idiopathic Arthritis
Mapped Trait(s) juvenile idiopathic arthritis (EFO_0002609)
Released in PGS: Feb. 27, 2020

Score Details

Score Construction
PGS Name GRS-JIA-20
Variants
Original Genome Build GRCh37
Number of Variants 26
Development Method
Name SparSNP
Parameters Lasso penalised linear regression (10-fold cross-validation) on genotypes . SNPs were initally selected by: significance p < 5e-5, and all SNPs within 1 Mb of the former.
PGS Source
PGS Catalog Publication (PGP) ID PGP000052
Citation (link to publication) Canovas R et al. medRxiv (2020) Preprint

Contributing Samples

Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
[
  • 2,324 cases
  • , 5,181 controls
]
,
45.7 % Male samples
European B58C, UKBS, WTCCC Similar cohort to PMID:27998952. Controls were sourced from th UK 1958 Birth cohort and UK Blood Services Common Controls, established as part of the WTCCC.

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)
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 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 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 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 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