Polygenic Score (PGS) ID: PGS001309

Predicted Trait
Reported Trait Other rheumatoid arthritis (time-to-event)
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1212
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC1212
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 323
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
[
  • 5,258 cases
  • , 264,446 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
PPM009039 PSS004193|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other rheumatoid arthritis AUROC: 0.69751 [0.65515, 0.73988] : 0.05129
Incremental AUROC (full-covars): -0.00017
PGS R2 (no covariates): 0.00056
PGS AUROC (no covariates): 0.52591 [0.47486, 0.57696]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009040 PSS004194|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other rheumatoid arthritis AUROC: 0.67331 [0.56418, 0.78244] : 0.07058
Incremental AUROC (full-covars): -0.02511
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50714 [0.3797, 0.63457]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009041 PSS004195|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other rheumatoid arthritis AUROC: 0.6872 [0.66167, 0.71273] : 0.04826
Incremental AUROC (full-covars): 0.02601
PGS R2 (no covariates): 0.01537
PGS AUROC (no covariates): 0.59782 [0.56885, 0.62679]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009042 PSS004196|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other rheumatoid arthritis AUROC: 0.70239 [0.66722, 0.73755] : 0.06164
Incremental AUROC (full-covars): -0.00362
PGS R2 (no covariates): 0.00158
PGS AUROC (no covariates): 0.53481 [0.4923, 0.57731]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009043 PSS004197|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other rheumatoid arthritis AUROC: 0.66538 [0.65101, 0.67976] : 0.03893
Incremental AUROC (full-covars): 0.03207
PGS R2 (no covariates): 0.01495
PGS AUROC (no covariates): 0.59784 [0.582, 0.61368]
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
PSS004193
[
  • 122 cases
  • , 6,375 controls
]
African unspecified UKB
PSS004194
[
  • 19 cases
  • , 1,685 controls
]
East Asian UKB
PSS004195
[
  • 409 cases
  • , 24,496 controls
]
European non-white British ancestry UKB
PSS004196
[
  • 197 cases
  • , 7,634 controls
]
South Asian UKB
PSS004197
[
  • 1,343 cases
  • , 66,082 controls
]
European white British ancestry UKB Testing cohort (heldout set)