Polygenic Score (PGS) ID: PGS000967

Predicted Trait
Reported Trait Coxarthrosis [arthrosis of hip] (time-to-event)
Mapped Trait(s) osteoarthritis, hip (EFO_1000786)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1221
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_HC1221
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 634
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
[
  • 10,909 cases
  • , 258,795 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
PPM007658 PSS004208|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.63448 [0.57611, 0.69284] : 0.02258
Incremental AUROC (full-covars): 0.01789
PGS R2 (no covariates): 0.0065
PGS AUROC (no covariates): 0.57452 [0.51022, 0.63883]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007659 PSS004209|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.67991 [0.52221, 0.83761] : 0.03974
Incremental AUROC (full-covars): 0.00141
PGS R2 (no covariates): 0.00044
PGS AUROC (no covariates): 0.52299 [0.39821, 0.64778]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007660 PSS004210|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.71352 [0.69682, 0.73022] : 0.07227
Incremental AUROC (full-covars): 0.00368
PGS R2 (no covariates): 0.00258
PGS AUROC (no covariates): 0.54164 [0.52116, 0.56213]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007661 PSS004211|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.72467 [0.66733, 0.78201] : 0.06598
Incremental AUROC (full-covars): -0.00237
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.50363 [0.44232, 0.56493]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007662 PSS004212|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.69051 [0.68108, 0.69995] : 0.06247
Incremental AUROC (full-covars): 0.00918
PGS R2 (no covariates): 0.00628
PGS AUROC (no covariates): 0.5611 [0.55051, 0.57168]
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
PSS004208
[
  • 85 cases
  • , 6,412 controls
]
African unspecified UKB
PSS004209
[
  • 16 cases
  • , 1,688 controls
]
East Asian UKB
PSS004210
[
  • 779 cases
  • , 24,126 controls
]
European non-white British ancestry UKB
PSS004211
[
  • 74 cases
  • , 7,757 controls
]
South Asian UKB
PSS004212
[
  • 2,783 cases
  • , 64,642 controls
]
European white British ancestry UKB Testing cohort (heldout set)