Polygenic Score (PGS) ID: PGS002106

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-ldpred2_calcium
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 702,009
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
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
PPM011708 PSS008269|
South Asian Ancestry|
5,484 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.2226 [0.1973, 0.2477] sex, age, birth date, deprivation index, 16 PCs —
PPM011709 PSS008047|
East Asian Ancestry|
1,563 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.2046 [0.1562, 0.2519] sex, age, birth date, deprivation index, 16 PCs —
PPM011710 PSS007833|
African Ancestry|
2,161 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.1002 [0.0581, 0.1419] sex, age, birth date, deprivation index, 16 PCs —
PPM011711 PSS008937|
African Ancestry|
3,403 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.1167 [0.0833, 0.1498] sex, age, birth date, deprivation index, 16 PCs —
PPM011707 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): 0.2067 [0.1471, 0.2649] sex, age, birth date, deprivation index, 16 PCs —
PPM011704 PSS009389|
European Ancestry|
17,443 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.2672 [0.2533, 0.2809] sex, age, birth date, deprivation index, 16 PCs —
PPM011705 PSS009163|
European Ancestry|
3,592 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.2911 [0.2608, 0.3208] sex, age, birth date, deprivation index, 16 PCs —
PPM011706 PSS008717|
European Ancestry|
5,801 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Calcium — — Partial Correlation (partial-r): 0.2562 [0.2319, 0.2801] 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 —
PSS008269 — — 5,484 individuals — South Asian India (South Asia) UKB —
PSS009389 — — 17,443 individuals — European UK (+ Ireland) UKB —
PSS008047 — — 1,563 individuals — East Asian China (East Asia) UKB —
PSS008717 — — 5,801 individuals — European Italy (South Europe) UKB —
PSS007833 — — 2,161 individuals — African American or Afro-Caribbean Carribean UKB —