Polygenic Score (PGS) ID: PGS002260

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Released in PGS Catalog: March 16, 2022
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Score Details

Score Construction
PGS Name PRS_RA
Development Method
Name PRSice-2
Parameters R2 = 0.027, P = 0.0026
Variants
Original Genome Build hg19
Number of Variants 43,784
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000286
Citation (link to publication) Honda S et al. Arthritis Rheumatol (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 72.1%
East Asian: 27.9%
80,799 individuals (100%)
Score Development/Training
East Asian: 100%
500 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002318
Europe PMC: 24390342
 58,284 individuals European NR
GWAS Catalog: GCST002318
Europe PMC: 24390342
 22,515 individuals East Asian NR
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
— 500 individuals,
14.2 % Male samples
 East Asian
(Japanese)		 IORRA Severe progressive group as patients with the top quartile of SHS (more than 35 points) and the non-severe progressive group as the remaining patients. Mean = 48.7 years
Sd = 12.6 years		 — — —

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
PPM012870 PSS009586|
East Asian Ancestry|
740 individuals
 PGP000286 |
Honda S et al. Arthritis Rheumatol (2022)
 Reported Trait: Severe radiographic progression in patients with rheumatoid arthritis — — OR (top vs 2nd quintile): 1.87 [1.11, 3.15] — —
PPM012871 PSS009586|
East Asian Ancestry|
740 individuals
 PGP000286 |
Honda S et al. Arthritis Rheumatol (2022)
 Reported Trait: Severe radiographic progression in patients with rheumatoid arthritis (age of onset <40 years) — — OR (top vs 2nd quintile): 6.29 [1.85, 21.4] — —
PPM012872 PSS009586|
East Asian Ancestry|
740 individuals
 PGP000286 |
Honda S et al. Arthritis Rheumatol (2022)
 Reported Trait: Severe radiographic progression in patients with rheumatoid arthritis OR: 1.3 [1.13, 1.5] — — Age of onset, sex, ever-smoker, ACPAs positivity, rheumatoid factor positivity, BMI, periodontitis, use of methotrexate, use of bDMARD, HLA-DRB1 (Ser11) —

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
PSS009586 Severe progressive group as patients with the top quartile of SHS (more than 35 points) and the non-severe progressive group as the remaining patients. — 740 individuals,
14.4 % Male samples
 Mean = 48.5 years
Sd = 12.4 years		 East Asian
(Japanese)		 — IORRA —