Polygenic Score (PGS) ID: PGS002745

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Released in PGS Catalog: Nov. 7, 2022
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Score Details

Score Construction
PGS Name metaPGS_RA
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2 threshold = 0.2; p-value threshold = 3e-03; variants were restricted to the top 5% score of IMPACT annotation (CD4+T T-bet); rare variants were excluded (<1% AF in EUR of 1KG phase 3).
Variants
Original Genome Build GRCh37
Number of Variants 2,575
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000357
Citation (link to publication) Ishigaki K et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • East Asian
  • African
  • South Asian
  • Greater Middle Eastern
276,020 individuals (100%)
PGS Evaluation
East Asian: 25%
European: 25%
Multi-ancestry (including European): 25%
  • European
  • East Asian
  • African
  • South Asian
  • Greater Middle Eastern
Multi-ancestry (excluding European): 25%
  • African
  • South Asian
  • Greater Middle Eastern
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 35,871 cases
  • , 240,149 controls
]
 European, East Asian, African unspecified, South Asian, Greater Middle Eastern (Middle Eastern, North African or Persian) BBJ

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
PPM014915 PSS009927|
Multi-ancestry (including European)|
7,460 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.65 Liability R2: 0.054 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds
PPM014916 PSS009930|
European Ancestry|
3,887 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.66 Liability R2: 0.059 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds
PPM014917 PSS009929|
East Asian Ancestry|
21,704 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.66 Liability R2: 0.057 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds
PPM014918 PSS009928|
Multi-ancestry (excluding European)|
1,304 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.59 Liability R2: 0.018 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds

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
PSS009927 — —
[
  • 969 cases
  • , 6,491 controls
]
 — European, East Asian, African unspecified, South Asian, Greater Middle Eastern (Middle Eastern, North African or Persian) — BBJ Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap
PSS009928 — —
[
  • 624 cases
  • , 680 controls
]
 — African unspecified, South Asian, Greater Middle Eastern (Middle Eastern, North African or Persian) — NR Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap
PSS009929 — —
[
  • 1,378 cases
  • , 20,326 controls
]
 — East Asian — BBJ Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap
PSS009930 — —
[
  • 894 cases
  • , 2,993 controls
]
 — European — NR Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap