Polygenic Score (PGS) ID: PGS001290

Predicted Trait
Reported Trait Osteoarthritis
Mapped Trait(s) osteoarthritis (MONDO_0005178)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC376
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_HC376
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 579
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%
269,704 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
—
[
  • 24,809 cases
  • , 244,895 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
PPM008948 PSS004461|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoarthritis — AUROC: 0.75416 [0.72668, 0.78163] R²: 0.12216
Incremental AUROC (full-covars): -3e-05
PGS R2 (no covariates): 0.00052
PGS AUROC (no covariates): 0.51951 [0.48655, 0.55248]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008949 PSS004462|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoarthritis — AUROC: 0.74181 [0.68024, 0.80338] R²: 0.09715
Incremental AUROC (full-covars): -0.00139
PGS R2 (no covariates): 0.00189
PGS AUROC (no covariates): 0.54245 [0.47153, 0.61338]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008950 PSS004463|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoarthritis — AUROC: 0.70244 [0.69044, 0.71444] R²: 0.08191
Incremental AUROC (full-covars): 0.0007
PGS R2 (no covariates): 0.0006
PGS AUROC (no covariates): 0.51661 [0.5024, 0.53082]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008951 PSS004464|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoarthritis — AUROC: 0.72534 [0.70181, 0.74887] R²: 0.09768
Incremental AUROC (full-covars): -0.00173
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49787 [0.47035, 0.52539]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008952 PSS004465|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoarthritis — AUROC: 0.67419 [0.66753, 0.68085] R²: 0.0674
Incremental AUROC (full-covars): 0.00134
PGS R2 (no covariates): 0.00109
PGS AUROC (no covariates): 0.52166 [0.51404, 0.52927]		 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
PSS004461 — —
[
  • 305 cases
  • , 6,192 controls
]
 — African unspecified — UKB —
PSS004462 — —
[
  • 56 cases
  • , 1,648 controls
]
 — East Asian — UKB —
PSS004463 — —
[
  • 1,688 cases
  • , 23,217 controls
]
 — European non-white British ancestry UKB —
PSS004464 — —
[
  • 425 cases
  • , 7,406 controls
]
 — South Asian — UKB —
PSS004465 — —
[
  • 6,097 cases
  • , 61,328 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)