Polygenic Score (PGS) ID: PGS001258

Predicted Trait
Reported Trait Radius fracture
Mapped Trait(s) radius fracture (EFO_0003957)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC57
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC57
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 365
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
[
  • 4,213 cases
  • , 265,491 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
PPM008795 PSS004531|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Fracture radius AUROC: 0.59097 [0.4568, 0.72514] : 0.0357
Incremental AUROC (full-covars): -0.02062
PGS R2 (no covariates): 0.00743
PGS AUROC (no covariates): 0.40578 [0.24928, 0.56228]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008796 PSS004532|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Fracture radius AUROC: 0.76104 [0.63028, 0.8918] : 0.07491
Incremental AUROC (full-covars): 0.01558
PGS R2 (no covariates): 0.00161
PGS AUROC (no covariates): 0.53524 [0.32644, 0.74404]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008797 PSS004533|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Fracture radius AUROC: 0.64808 [0.61916, 0.67701] : 0.03028
Incremental AUROC (full-covars): 0.0032
PGS R2 (no covariates): 0.00384
PGS AUROC (no covariates): 0.55216 [0.52295, 0.58137]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008798 PSS004534|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Fracture radius AUROC: 0.66735 [0.59592, 0.73878] : 0.03501
Incremental AUROC (full-covars): -0.00475
PGS R2 (no covariates): 0.00103
PGS AUROC (no covariates): 0.52544 [0.45652, 0.59436]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008799 PSS004535|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Fracture radius AUROC: 0.64876 [0.63106, 0.66645] : 0.02773
Incremental AUROC (full-covars): 0.00901
PGS R2 (no covariates): 0.00379
PGS AUROC (no covariates): 0.55608 [0.53855, 0.57362]
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
PSS004531
[
  • 15 cases
  • , 6,482 controls
]
African unspecified UKB
PSS004532
[
  • 10 cases
  • , 1,694 controls
]
East Asian UKB
PSS004533
[
  • 375 cases
  • , 24,530 controls
]
European non-white British ancestry UKB
PSS004534
[
  • 61 cases
  • , 7,770 controls
]
South Asian UKB
PSS004535
[
  • 1,022 cases
  • , 66,403 controls
]
European white British ancestry UKB Testing cohort (heldout set)