Polygenic Score (PGS) ID: PGS001135

Predicted Trait
Reported Trait Arthritis (nos)
Mapped Trait(s) arthritis (EFO_0005856)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC78
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_HC78
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,028
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
[
  • 16,110 cases
  • , 253,594 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
PPM008403 PSS004627|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Arthritis (nos) AUROC: 0.7166 [0.69191, 0.7413] : 0.0961
Incremental AUROC (full-covars): -0.00204
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50267 [0.47421, 0.53114]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008404 PSS004628|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Arthritis (nos) AUROC: 0.78855 [0.73521, 0.8419] : 0.13042
Incremental AUROC (full-covars): -0.00593
PGS R2 (no covariates): 0.00821
PGS AUROC (no covariates): 0.42483 [0.32454, 0.52511]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008405 PSS004629|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Arthritis (nos) AUROC: 0.67424 [0.65969, 0.68878] : 0.05468
Incremental AUROC (full-covars): 0.00314
PGS R2 (no covariates): 0.00291
PGS AUROC (no covariates): 0.53928 [0.52302, 0.55554]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008406 PSS004630|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Arthritis (nos) AUROC: 0.71014 [0.68888, 0.73139] : 0.08893
Incremental AUROC (full-covars): 0.00207
PGS R2 (no covariates): 0.00153
PGS AUROC (no covariates): 0.52639 [0.5015, 0.55128]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008407 PSS004631|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Arthritis (nos) AUROC: 0.64961 [0.64135, 0.65786] : 0.04342
Incremental AUROC (full-covars): 0.00228
PGS R2 (no covariates): 0.00147
PGS AUROC (no covariates): 0.52671 [0.51771, 0.53571]
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
PSS004627
[
  • 407 cases
  • , 6,090 controls
]
African unspecified UKB
PSS004628
[
  • 36 cases
  • , 1,668 controls
]
East Asian UKB
PSS004629
[
  • 1,244 cases
  • , 23,661 controls
]
European non-white British ancestry UKB
PSS004630
[
  • 538 cases
  • , 7,293 controls
]
South Asian UKB
PSS004631
[
  • 4,088 cases
  • , 63,337 controls
]
European white British ancestry UKB Testing cohort (heldout set)