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
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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_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. 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
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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
—
[
  • 10,909 cases
  • , 258,795 controls
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM007658PSS004208|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE coxarthrosis [arthrosis of hip]—AUROC: 0.63448 [0.57611, 0.69284]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007659PSS004209|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE coxarthrosis [arthrosis of hip]—AUROC: 0.67991 [0.52221, 0.83761]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007660PSS004210|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE coxarthrosis [arthrosis of hip]—AUROC: 0.71352 [0.69682, 0.73022]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007661PSS004211|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE coxarthrosis [arthrosis of hip]—AUROC: 0.72467 [0.66733, 0.78201]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007662PSS004212|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE coxarthrosis [arthrosis of hip]—AUROC: 0.69051 [0.68108, 0.69995]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
]
—Europeannon-white British ancestryUKB—
PSS004211——
[
  • 74 cases
  • , 7,757 controls
]
—South Asian—UKB—
PSS004212——
[
  • 2,783 cases
  • , 64,642 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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