Polygenic Score (PGS) ID: PGS001138

Predicted Trait
Reported Trait Rheumatoid factor [> 16 IU/mL]
Mapped Trait(s) rheumatoid factor measurement (EFO_0005767)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN10030820
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN10030820
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 456
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%
257,087 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 13,354 cases
  • , 243,733 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
PPM008417 PSS003622|
African Ancestry|
6,090 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Rheumatoid factor > 16 IU/mL — AUROC: 0.59937 [0.56738, 0.63135] R²: 0.01517
Incremental AUROC (full-covars): -0.0001
PGS R2 (no covariates): 0.00074
PGS AUROC (no covariates): 0.52274 [0.48589, 0.55958]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008418 PSS003623|
East Asian Ancestry|
1,618 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Rheumatoid factor > 16 IU/mL — AUROC: 0.62134 [0.5547, 0.68798] R²: 0.0451
Incremental AUROC (full-covars): 0.02013
PGS R2 (no covariates): 0.00611
PGS AUROC (no covariates): 0.561 [0.49101, 0.631]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008419 PSS003624|
European Ancestry|
23,747 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Rheumatoid factor > 16 IU/mL — AUROC: 0.61687 [0.6002, 0.63355] R²: 0.02493
Incremental AUROC (full-covars): 0.04213
PGS R2 (no covariates): 0.01627
PGS AUROC (no covariates): 0.59686 [0.57968, 0.61405]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008420 PSS003625|
South Asian Ancestry|
7,429 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Rheumatoid factor > 16 IU/mL — AUROC: 0.59949 [0.57257, 0.62641] R²: 0.01901
Incremental AUROC (full-covars): 0.00874
PGS R2 (no covariates): 0.00434
PGS AUROC (no covariates): 0.54845 [0.52086, 0.57604]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008421 PSS003626|
European Ancestry|
64,281 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Rheumatoid factor > 16 IU/mL — AUROC: 0.60052 [0.59084, 0.6102] R²: 0.0181
Incremental AUROC (full-covars): 0.04923
PGS R2 (no covariates): 0.01405
PGS AUROC (no covariates): 0.58407 [0.57416, 0.59397]		 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
PSS003622 — —
[
  • 282 cases
  • , 5,808 controls
]
 — African unspecified — UKB —
PSS003623 — —
[
  • 79 cases
  • , 1,539 controls
]
 — East Asian — UKB —
PSS003624 — —
[
  • 1,087 cases
  • , 22,660 controls
]
 — European non-white British ancestry UKB —
PSS003625 — —
[
  • 395 cases
  • , 7,034 controls
]
 — South Asian — UKB —
PSS003626 — —
[
  • 3,345 cases
  • , 60,936 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)