Polygenic Score (PGS) ID: PGS000676

Predicted Trait
Reported Trait Calcium [mmol/L]
Mapped Trait(s) calcium measurement (EFO_0004838)
Released in PGS Catalog: Feb. 3, 2021
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Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Calcium
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 12,334
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 45.5%
African: 18.2%
East Asian: 18.2%
South Asian: 18.2%
11 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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001404 PSS000657|
African Ancestry|
5,576 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Calcium [mmol/L] — — R²: 0.07349
Spearman's ρ: 0.11		 Age, sex, PCs(1-40) —
PPM001439 PSS000658|
East Asian Ancestry|
987 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Calcium [mmol/L] — — R²: 0.10943
Spearman's ρ: 0.225		 Age, sex, PCs(1-40) —
PPM001474 PSS000659|
European Ancestry|
21,544 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Calcium [mmol/L] — — R²: 0.11196
Spearman's ρ: 0.25		 Age, sex, PCs(1-40) —
PPM001509 PSS000660|
South Asian Ancestry|
6,696 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Calcium [mmol/L] — — R²: 0.0961
Spearman's ρ: 0.226		 Age, sex, PCs(1-40) —
PPM001544 PSS000661|
European Ancestry|
58,264 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Calcium [mmol/L] — — R²: 0.11497
Spearman's ρ: 0.26		 Age, sex, PCs(1-40) —
PPM001590 PSS000796|
European Ancestry|
2,072 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Calcium [mmol/L] — — Spearman's ρ: 0.202 Age, sex —
PPM007305 PSS007121|
African Ancestry|
5,658 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Calcium — — R²: 0.03291 [0.02438, 0.04144]
Incremental R2 (full-covars): 0.01221
PGS R2 (no covariates): 0.01435 [0.00861, 0.02009]		 age, sex, UKB array type, Genotype PCs —
PPM007306 PSS007122|
East Asian Ancestry|
1,475 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Calcium — — R²: 0.05488 [0.0339, 0.07586]
Incremental R2 (full-covars): 0.02744
PGS R2 (no covariates): 0.03682 [0.01931, 0.05434]		 age, sex, UKB array type, Genotype PCs —
PPM007307 PSS007123|
European Ancestry|
21,751 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Calcium — — R²: 0.0574 [0.05179, 0.06301]
Incremental R2 (full-covars): 0.04912
PGS R2 (no covariates): 0.05876 [0.05309, 0.06442]		 age, sex, UKB array type, Genotype PCs —
PPM007308 PSS007124|
South Asian Ancestry|
6,790 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Calcium — — R²: 0.04643 [0.03734, 0.05553]
Incremental R2 (full-covars): 0.03689
PGS R2 (no covariates): 0.04361 [0.03477, 0.05246]		 age, sex, UKB array type, Genotype PCs —
PPM007309 PSS007125|
European Ancestry|
59,074 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Calcium — — R²: 0.06293 [0.05938, 0.06648]
Incremental R2 (full-covars): 0.05233
PGS R2 (no covariates): 0.06188 [0.05836, 0.06541]		 age, sex, UKB array type, Genotype 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
PSS000657 — — 5,576 individuals — African unspecified — UKB —
PSS000658 — — 987 individuals — East Asian — UKB —
PSS000659 — — 21,544 individuals — European Non-British White UKB —
PSS000660 — — 6,696 individuals — South Asian — UKB —
PSS000661 — — 58,264 individuals — European
(British)		 — UKB —
PSS007123 — — 21,751 individuals — European non-white British ancestry UKB —
PSS000796 — — 2,072 individuals — European Participants self-identifying as white MESA —
PSS007121 — — 5,658 individuals — African unspecified — UKB —
PSS007122 — — 1,475 individuals — East Asian — UKB —
PSS007124 — — 6,790 individuals — South Asian — UKB —
PSS007125 — — 59,074 individuals — European white British ancestry UKB Testing cohort (heldout set)