Polygenic Score (PGS) ID: PGS001274

Predicted Trait
Reported Trait Osteoporosis without pathological fracture (time-to-event)
Mapped Trait(s) osteoporosis (EFO_0003882)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1268
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_HC1268
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,270
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
—
[
  • 9,433 cases
  • , 260,271 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
PPM008868 PSS004243|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.74925 [0.69511, 0.80339] R²: 0.08288
Incremental AUROC (full-covars): -0.00137
PGS R2 (no covariates): 0.00122
PGS AUROC (no covariates): 0.51972 [0.45381, 0.58563]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008869 PSS004244|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.81083 [0.73828, 0.88338] R²: 0.14813
Incremental AUROC (full-covars): -0.0044
PGS R2 (no covariates): 9e-05
PGS AUROC (no covariates): 0.50546 [0.40063, 0.61028]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008870 PSS004245|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.79652 [0.78363, 0.8094] R²: 0.15697
Incremental AUROC (full-covars): 0.00777
PGS R2 (no covariates): 0.00945
PGS AUROC (no covariates): 0.57595 [0.55816, 0.59374]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008871 PSS004246|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.81463 [0.78571, 0.84355] R²: 0.16403
Incremental AUROC (full-covars): -0.00198
PGS R2 (no covariates): 0.00037
PGS AUROC (no covariates): 0.51416 [0.47459, 0.55374]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008872 PSS004247|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.77492 [0.76604, 0.7838] R²: 0.12779
Incremental AUROC (full-covars): 0.00797
PGS R2 (no covariates): 0.0089
PGS AUROC (no covariates): 0.57419 [0.56237, 0.586]		 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
PSS004243 — —
[
  • 85 cases
  • , 6,412 controls
]
 — African unspecified — UKB —
PSS004244 — —
[
  • 30 cases
  • , 1,674 controls
]
 — East Asian — UKB —
PSS004245 — —
[
  • 1,020 cases
  • , 23,885 controls
]
 — European non-white British ancestry UKB —
PSS004246 — —
[
  • 205 cases
  • , 7,626 controls
]
 — South Asian — UKB —
PSS004247 — —
[
  • 2,326 cases
  • , 65,099 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)