Polygenic Score (PGS) ID: PGS000325

Predicted Trait
Reported Trait Oligoarthritis Juvenile Idiophatic Arthritis
Mapped Trait(s) oligoarticular juvenile idiopathic arthritis (EFO_1002019)
Released in PGS Catalog: Sept. 18, 2020
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Terms and Licenses
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Score Details

Score Construction
PGS Name GRS-JIA-Oli-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 21
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%
6,137 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development 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
[
  • 956 cases
  • , 5,181 controls
]
,
47.55 % 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
PPM000875 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 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
PPM000869 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 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]

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
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
PSS000433 Diagnosis of JIA by a paediatric rheumatologist.
[
  • 159 cases
  • , 578 controls
]
,
51.15 % Male samples
European CLARITY Cohort description (PMID): 23153063