Polygenic Score (PGS) ID: PGS000326

Predicted Trait
Reported Trait Rheumatoid-factor-negative Polyarthritis (Juvenile Idiophatic Arthritis)
Mapped Trait(s) polyarticular juvenile idiopathic arthritis, rheumatoid factor negative (EFO_1002020)
Released in PGS Catalog: Sept. 18, 2020
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Score Details

Score Construction
PGS Name GRS-JIA-RFN-20
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.
Variants
Original Genome Build GRCh37
Number of Variants 12
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000052
Citation (link to publication) Cánovas R et al. Ann Rheum Dis (2020)
Ancestry Distribution
Score Development/Training
European: 100%
5,733 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 27998952
[
  • 552 cases
  • , 5,181 controls
]
,
48.19 % 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) 		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 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 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] — — —
PPM000877 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 —
PPM000871 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
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 —
PSS000434 Diagnosis of JIA by a paediatric rheumatologist. —
[
  • 75 cases
  • , 578 controls
]
,
54.82 % Male samples
 — European — CLARITY Cohort description (PMID): 23153063