Polygenic Score (PGS) ID: PGS001110

Predicted Trait
Reported Trait Reactive arthropathies (time-to-event)
Mapped Trait(s) reactive arthritis (EFO_0007460)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1209
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_HC1209
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6
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: 50%
African: 25%
South Asian: 25%
4 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
[
  • 137 cases
  • , 269,567 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
PPM008289 PSS004183|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE reactive arthropathies AUROC: 0.9594 [0.92062, 0.99818] : 0.17918
Incremental AUROC (full-covars): 0.00395
PGS R2 (no covariates): 0.00991
PGS AUROC (no covariates): 0.72061 [0.49213, 0.9491]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008290 PSS004185|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE reactive arthropathies AUROC: 0.77096 [0.63921, 0.90271] : 0.09743
Incremental AUROC (full-covars): 0.03274
PGS R2 (no covariates): 0.03411
PGS AUROC (no covariates): 0.65137 [0.47674, 0.826]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008291 PSS004186|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE reactive arthropathies AUROC: 0.94552 [0.83969, 1.0] : 0.25627
Incremental AUROC (full-covars): 0.00045
PGS R2 (no covariates): 0.00071
PGS AUROC (no covariates): 0.67786 [0.66768, 0.68805]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008292 PSS004187|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE reactive arthropathies AUROC: 0.6839 [0.58647, 0.78132] : 0.03053
Incremental AUROC (full-covars): 0.07922
PGS R2 (no covariates): 0.02879
PGS AUROC (no covariates): 0.66167 [0.54859, 0.77475]
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
PSS004183
[
  • 3 cases
  • , 6,494 controls
]
African unspecified UKB
PSS004185
[
  • 12 cases
  • , 24,893 controls
]
European non-white British ancestry UKB
PSS004186
[
  • 2 cases
  • , 7,829 controls
]
South Asian UKB
PSS004187
[
  • 30 cases
  • , 67,395 controls
]
European white British ancestry UKB Testing cohort (heldout set)