Polygenic Score (PGS) ID: PGS001310

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC430
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_HC430
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 175
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
[
  • 5,062 cases
  • , 264,642 controls
]
European white British ancestry UKB

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
PPM009044 PSS004491|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Rheumatoid arthritis AUROC: 0.70522 [0.66309, 0.74736] : 0.0544
Incremental AUROC (full-covars): 0.00203
PGS R2 (no covariates): 0.00109
PGS AUROC (no covariates): 0.53147 [0.47999, 0.58294]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009045 PSS004492|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Rheumatoid arthritis AUROC: 0.66116 [0.54578, 0.77655] : 0.06929
Incremental AUROC (full-covars): -0.02514
PGS R2 (no covariates): 0.00033
PGS AUROC (no covariates): 0.52178 [0.38366, 0.6599]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009046 PSS004493|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Rheumatoid arthritis AUROC: 0.68857 [0.6632, 0.71393] : 0.04919
Incremental AUROC (full-covars): 0.02092
PGS R2 (no covariates): 0.01316
PGS AUROC (no covariates): 0.58714 [0.55751, 0.61676]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009047 PSS004494|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Rheumatoid arthritis AUROC: 0.70402 [0.66905, 0.73899] : 0.06207
Incremental AUROC (full-covars): -0.0019
PGS R2 (no covariates): 0.00142
PGS AUROC (no covariates): 0.53137 [0.48984, 0.57291]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009048 PSS004495|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Rheumatoid arthritis AUROC: 0.66508 [0.65049, 0.67967] : 0.03894
Incremental AUROC (full-covars): 0.03077
PGS R2 (no covariates): 0.01509
PGS AUROC (no covariates): 0.60018 [0.58428, 0.61607]
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
PSS004491
[
  • 118 cases
  • , 6,379 controls
]
African unspecified UKB
PSS004492
[
  • 18 cases
  • , 1,686 controls
]
East Asian UKB
PSS004493
[
  • 399 cases
  • , 24,506 controls
]
European non-white British ancestry UKB
PSS004494
[
  • 194 cases
  • , 7,637 controls
]
South Asian UKB
PSS004495
[
  • 1,301 cases
  • , 66,124 controls
]
European white British ancestry UKB Testing cohort (heldout set)