Polygenic Score (PGS) ID: PGS001893

Predicted Trait
Reported Trait Calcium
Mapped Trait(s) calcium measurement (EFO_0004838)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_calcium
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 48,395
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: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
391,124 individuals European UK (+ Ireland) 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
PPM010028 PSS009389|
European Ancestry|
17,443 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2668 [0.2529, 0.2805] sex, age, birth date, deprivation index, 16 PCs
PPM010029 PSS009163|
European Ancestry|
3,592 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2822 [0.2517, 0.3121] sex, age, birth date, deprivation index, 16 PCs
PPM010030 PSS008717|
European Ancestry|
5,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.252 [0.2277, 0.276] sex, age, birth date, deprivation index, 16 PCs
PPM010031 PSS008491|
Greater Middle Eastern Ancestry|
1,035 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2261 [0.1669, 0.2837] sex, age, birth date, deprivation index, 16 PCs
PPM010032 PSS008269|
South Asian Ancestry|
5,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.241 [0.2159, 0.2658] sex, age, birth date, deprivation index, 16 PCs
PPM010033 PSS008047|
East Asian Ancestry|
1,563 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2155 [0.1674, 0.2626] sex, age, birth date, deprivation index, 16 PCs
PPM010034 PSS007833|
African Ancestry|
2,161 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.1173 [0.0753, 0.1589] sex, age, birth date, deprivation index, 16 PCs
PPM010035 PSS008937|
African Ancestry|
3,403 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.1184 [0.085, 0.1515] sex, age, birth date, deprivation index, 16 PCs

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
PSS008937 3,403 individuals African unspecified Nigeria (West Africa) UKB
PSS008491 1,035 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009163 3,592 individuals European Poland (NE Europe) UKB
PSS008717 5,801 individuals European Italy (South Europe) UKB
PSS009389 17,443 individuals European UK (+ Ireland) UKB
PSS008269 5,484 individuals South Asian India (South Asia) UKB
PSS008047 1,563 individuals East Asian China (East Asia) UKB
PSS007833 2,161 individuals African American or Afro-Caribbean Carribean UKB