Polygenic Score (PGS) ID: PGS001273

Predicted Trait
Reported Trait Osteoporosis
Mapped Trait(s) osteoporosis (EFO_0003882)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC22
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_HC22
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 316
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
—
[
  • 8,654 cases
  • , 261,050 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
PPM008863 PSS004369|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.75545 [0.70356, 0.80735] R²: 0.08703
Incremental AUROC (full-covars): -0.00106
PGS R2 (no covariates): 0.00045
PGS AUROC (no covariates): 0.51891 [0.45926, 0.57855]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008864 PSS004370|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.85769 [0.79768, 0.9177] R²: 0.20187
Incremental AUROC (full-covars): -0.00208
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50947 [0.39122, 0.62773]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008865 PSS004371|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.78972 [0.77584, 0.8036] R²: 0.14567
Incremental AUROC (full-covars): 0.00477
PGS R2 (no covariates): 0.00688
PGS AUROC (no covariates): 0.5685 [0.55009, 0.58691]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008866 PSS004372|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.82202 [0.79395, 0.85009] R²: 0.17031
Incremental AUROC (full-covars): 0.00037
PGS R2 (no covariates): 5e-05
PGS AUROC (no covariates): 0.50461 [0.4652, 0.54402]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008867 PSS004373|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.7643 [0.75478, 0.77381] R²: 0.1146
Incremental AUROC (full-covars): 0.00589
PGS R2 (no covariates): 0.00698
PGS AUROC (no covariates): 0.5684 [0.55603, 0.58076]		 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
PSS004369 — —
[
  • 92 cases
  • , 6,405 controls
]
 — African unspecified — UKB —
PSS004370 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004371 — —
[
  • 932 cases
  • , 23,973 controls
]
 — European non-white British ancestry UKB —
PSS004372 — —
[
  • 195 cases
  • , 7,636 controls
]
 — South Asian — UKB —
PSS004373 — —
[
  • 2,151 cases
  • , 65,274 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)