Polygenic Score (PGS) ID: PGS001311

Predicted Trait
Reported Trait Seropositive rheumatoid arthritis (time-to-event)
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1211
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_HC1211
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 50%
African: 25%
South Asian: 25%
4 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
—
[
  • 509 cases
  • , 269,195 controls
]
 European UKB — — — white British ancestry —

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
PPM009049 PSS004188|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seropositive rheumatoid arthritis — AUROC: 0.90345 [0.82233, 0.98457] R²: 0.16794
Incremental AUROC (full-covars): -0.00669
PGS R2 (no covariates): 0.01613
PGS AUROC (no covariates): 0.39273 [0.11505, 0.67041]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009050 PSS004190|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seropositive rheumatoid arthritis — AUROC: 0.76787 [0.6839, 0.85184] R²: 0.08412
Incremental AUROC (full-covars): 0.0418
PGS R2 (no covariates): 0.05847
PGS AUROC (no covariates): 0.73164 [0.63667, 0.82662]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009051 PSS004191|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seropositive rheumatoid arthritis — AUROC: 0.76865 [0.6608, 0.87651] R²: 0.08089
Incremental AUROC (full-covars): -0.00731
PGS R2 (no covariates): 0.00567
PGS AUROC (no covariates): 0.50626 [0.35145, 0.66107]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009052 PSS004192|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seropositive rheumatoid arthritis — AUROC: 0.73785 [0.69634, 0.77936] R²: 0.05309
Incremental AUROC (full-covars): 0.09202
PGS R2 (no covariates): 0.04612
PGS AUROC (no covariates): 0.7072 [0.65945, 0.75495]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004188 — —
[
  • 5 cases
  • , 6,492 controls
]
 — African unspecified — UKB —
PSS004190 — —
[
  • 32 cases
  • , 24,873 controls
]
 — European non-white British ancestry UKB —
PSS004191 — —
[
  • 18 cases
  • , 7,813 controls
]
 — South Asian — UKB —
PSS004192 — —
[
  • 127 cases
  • , 67,298 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)