Polygenic Score (PGS) ID: PGS001026

Predicted Trait
Reported Trait Forearm or wrist fracture
Mapped Trait(s) upper extremity fracture (EFO_0009514)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC83
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_HC83
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 45
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
—
[
  • 5,543 cases
  • , 264,161 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
PPM007893 PSS004647|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fracture forearm / wrist — AUROC: 0.57316 [0.48864, 0.65768] R²: 0.01719
Incremental AUROC (full-covars): 0.0117
PGS R2 (no covariates): 0.00036
PGS AUROC (no covariates): 0.49899 [0.40484, 0.59313]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007894 PSS004648|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fracture forearm / wrist — AUROC: 0.75931 [0.65302, 0.8656] R²: 0.07041
Incremental AUROC (full-covars): 0.00842
PGS R2 (no covariates): 0.0034
PGS AUROC (no covariates): 0.56595 [0.41049, 0.72141]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007895 PSS004649|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fracture forearm / wrist — AUROC: 0.61781 [0.5913, 0.64433] R²: 0.01996
Incremental AUROC (full-covars): 0.00765
PGS R2 (no covariates): 0.00371
PGS AUROC (no covariates): 0.55337 [0.52778, 0.57896]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007896 PSS004650|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fracture forearm / wrist — AUROC: 0.60309 [0.54059, 0.6656] R²: 0.01453
Incremental AUROC (full-covars): -0.01824
PGS R2 (no covariates): 0.00052
PGS AUROC (no covariates): 0.48161 [0.4179, 0.54533]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007897 PSS004651|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fracture forearm / wrist — AUROC: 0.61632 [0.60022, 0.63241] R²: 0.01772
Incremental AUROC (full-covars): 0.00729
PGS R2 (no covariates): 0.0027
PGS AUROC (no covariates): 0.54479 [0.52931, 0.56027]		 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
PSS004647 — —
[
  • 34 cases
  • , 6,463 controls
]
 — African unspecified — UKB —
PSS004648 — —
[
  • 12 cases
  • , 1,692 controls
]
 — East Asian — UKB —
PSS004649 — —
[
  • 490 cases
  • , 24,415 controls
]
 — European non-white British ancestry UKB —
PSS004650 — —
[
  • 82 cases
  • , 7,749 controls
]
 — South Asian — UKB —
PSS004651 — —
[
  • 1,349 cases
  • , 66,076 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)