| Predicted Trait | |
| Reported Trait | Right heel bone mineral density (BMD) T-score, automated |
| Mapped Trait(s) | heel bone mineral density (EFO_0009270) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4125 |
| Score Construction | |
| PGS Name | GBE_INI4125 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 9,753 |
| 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% 103,563 individuals (100%) |
| PGS Evaluation | European: 40% African: 20% East Asian: 20% South Asian: 20% 5 Sample Sets |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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|---|---|---|---|---|---|---|---|---|
| — | 103,563 individuals | European | UKB | — | — | — | white British ancestry | — |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
|
PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM007953 | PSS007326| African Ancestry| 3,592 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) | — | — | R²: 0.02463 [0.01719, 0.03207] Incremental R2 (full-covars): 0.00616 PGS R2 (no covariates): 0.00698 [0.00294, 0.01101] | age, sex, UKB array type, Genotype PCs | — |
| PPM007954 | PSS007327| East Asian Ancestry| 782 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) | — | — | R²: 0.09885 [0.072, 0.1257] Incremental R2 (full-covars): 0.07541 PGS R2 (no covariates): 0.07555 [0.05147, 0.09963] | age, sex, UKB array type, Genotype PCs | — |
| PPM007955 | PSS007328| European Ancestry| 10,633 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) | — | — | R²: 0.1752 [0.16663, 0.18378] Incremental R2 (full-covars): 0.11145 PGS R2 (no covariates): 0.11271 [0.10531, 0.12011] | age, sex, UKB array type, Genotype PCs | — |
| PPM007956 | PSS007329| South Asian Ancestry| 5,041 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) | — | — | R²: 0.08262 [0.07095, 0.0943] Incremental R2 (full-covars): 0.05817 PGS R2 (no covariates): 0.05815 [0.0481, 0.06821] | age, sex, UKB array type, Genotype PCs | — |
| PPM007957 | PSS007330| European Ancestry| 25,728 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) | — | — | R²: 0.19359 [0.18823, 0.19894] Incremental R2 (full-covars): 0.1242 PGS R2 (no covariates): 0.12266 [0.11802, 0.1273] | age, sex, UKB array type, Genotype PCs | — |
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
|
|---|---|---|---|---|---|---|---|---|
| PSS007326 | — | — | 3,592 individuals | — | African unspecified | — | UKB | — |
| PSS007327 | — | — | 782 individuals | — | East Asian | — | UKB | — |
| PSS007328 | — | — | 10,633 individuals | — | European | non-white British ancestry | UKB | — |
| PSS007329 | — | — | 5,041 individuals | — | South Asian | — | UKB | — |
| PSS007330 | — | — | 25,728 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |