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: Sept. 18, 2020
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Score Details

Score Construction
PGS Name GRS-JIA-RFN-20
Variants
Original Genome Build GRCh37
Number of Variants 12
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) Cánovas R et al. Ann Rheum Dis (2020)

Contributing Samples

Score Development/Training
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
[
  • 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 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
PPM000878 PSS000434 PGP000052
Cánovas R et al. (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
PPM000877 PSS000431 PGP000052
Cánovas R et al. (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
PPM000872 PSS000434 PGP000052
Cánovas R et al. (2020)
Reported Trait: Rheumatoid-factor-negative Polyarthritis OR: 1.69[1.42, 2.02] AUROC: 0.66[0.59, 0.73]
PPM000871 PSS000431 PGP000052
Cánovas R et al. (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 ID)
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