Polygenic Score (PGS) ID: PGS001955

Predicted Trait
Reported Trait Heel bone mineral density (BMD)
Mapped Trait(s) heel bone mineral density (EFO_0009270)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_heel_BMD
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 73,565
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 33.3%
African: 22.2%
East Asian: 22.2%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM010515 PSS009446|
European Ancestry|
11,484 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.4537 [0.4391, 0.4682] sex, age, birth date, deprivation index, 16 PCs —
PPM010516 PSS009220|
European Ancestry|
2,146 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.4397 [0.4048, 0.4734] sex, age, birth date, deprivation index, 16 PCs —
PPM010519 PSS008326|
South Asian Ancestry|
1,972 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.3477 [0.3081, 0.3861] sex, age, birth date, deprivation index, 16 PCs —
PPM010520 PSS008103|
East Asian Ancestry|
820 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.3057 [0.2415, 0.3672] sex, age, birth date, deprivation index, 16 PCs —
PPM010521 PSS007890|
African Ancestry|
790 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.1895 [0.1204, 0.2567] sex, age, birth date, deprivation index, 16 PCs —
PPM010522 PSS008994|
African Ancestry|
1,406 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.1746 [0.1231, 0.2252] sex, age, birth date, deprivation index, 16 PCs —
PPM010517 PSS008774|
European Ancestry|
3,461 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.3929 [0.3643, 0.4208] sex, age, birth date, deprivation index, 16 PCs —
PPM010518 PSS008548|
Greater Middle Eastern Ancestry|
506 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — Partial Correlation (partial-r): 0.2944 [0.211, 0.3736] sex, age, birth date, deprivation index, 16 PCs —
PPM022387 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of vertebral column without mention of spinal cord injury (Phecode 805) OR: 1.93 — — — —
PPM022388 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Osteoporosis (Phecode 743.1) OR: 1.68 — — — —
PPM022389 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Osteoporosis NOS (Phecode 743.11) OR: 1.68 — — — —
PPM022390 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Osteoporosis (Phecode 743) OR: 1.61 — — — —
PPM022391 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of upper limb (Phecode 803) OR: 2.93 — — — —
PPM022392 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of radius and ulna (Phecode 803.2) OR: 3.64 — — — —
PPM022393 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of lower limb (Phecode 800) OR: 2.51 — — — —
PPM022394 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of humerus (Phecode 803.1) OR: 3.54 — — — —
PPM022395 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of ankle and foot (Phecode 801) OR: 2.78 — — — —
PPM022396 PSS011935|
East Asian Ancestry|
3,744 individuals
 PGP000710 |
Chen JJ et al. Arch Osteoporos (2023)
|Ext.		 Reported Trait: Fracture of tibia and fibula (Phecode 800.3) OR: 4.45 — — — —

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
PSS009220 — — 2,146 individuals — European Poland (NE Europe) UKB —
PSS008548 — — 506 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008326 — — 1,972 individuals — South Asian India (South Asia) UKB —
PSS009446 — — 11,484 individuals — European UK (+ Ireland) UKB —
PSS008103 — — 820 individuals — East Asian China (East Asia) UKB —
PSS008774 — — 3,461 individuals — European Italy (South Europe) UKB —
PSS011935 — — 3,744 individuals,
24.0 % Male samples
 Mean = 66.7 years East Asian — TPMI —
PSS007890 — — 790 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008994 — — 1,406 individuals — African unspecified Nigeria (West Africa) UKB —