Polygenic Score (PGS) ID: PGS000677

Predicted Trait
Reported Trait Cholesterol [mmol/L] (statin adjusted)
Mapped Trait(s) total cholesterol measurement (EFO_0004574)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Cholesterol_adjstatins
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 17,204
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: 50%
African: 16.7%
East Asian: 16.7%
South Asian: 16.7%
12 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
PPM001405 PSS000662|
African Ancestry|
6,014 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — R²: 0.1282
Spearman's ρ: 0.26		 Age, sex, PCs(1-40) —
PPM001440 PSS000663|
East Asian Ancestry|
1,082 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — R²: 0.17187
Spearman's ρ: 0.314		 Age, sex, PCs(1-40) —
PPM001475 PSS000664|
European Ancestry|
23,581 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — R²: 0.26423
Spearman's ρ: 0.421		 Age, sex, PCs(1-40) —
PPM001510 PSS000665|
South Asian Ancestry|
7,336 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — R²: 0.1266
Spearman's ρ: 0.3		 Age, sex, PCs(1-40) —
PPM001545 PSS000666|
European Ancestry|
63,794 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — R²: 0.26395
Spearman's ρ: 0.429		 Age, sex, PCs(1-40) —
PPM001574 PSS000798|
European Ancestry|
2,004 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — Spearman's ρ: 0.173 Age, sex —
PPM001573 PSS000797|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholesterol [mmol/L] (statin adjusted) — — Spearman's ρ: 0.184 Age, sex —
PPM007310 PSS007126|
African Ancestry|
6,097 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Cholesterol — — R²: 0.04241 [0.03283, 0.052]
Incremental R2 (full-covars): 0.03032
PGS R2 (no covariates): 0.05951 [0.04835, 0.07066]		 age, sex, UKB array type, Genotype PCs —
PPM007311 PSS007127|
East Asian Ancestry|
1,616 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Cholesterol — — R²: 0.06535 [0.04271, 0.08799]
Incremental R2 (full-covars): 0.03188
PGS R2 (no covariates): 0.07616 [0.052, 0.10032]		 age, sex, UKB array type, Genotype PCs —
PPM007312 PSS007128|
European Ancestry|
23,774 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Cholesterol — — R²: 0.07903 [0.0726, 0.08546]
Incremental R2 (full-covars): 0.04607
PGS R2 (no covariates): 0.10696 [0.0997, 0.11421]		 age, sex, UKB array type, Genotype PCs —
PPM007313 PSS007129|
South Asian Ancestry|
7,426 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Cholesterol — — R²: 0.05766 [0.04764, 0.06768]
Incremental R2 (full-covars): 0.02119
PGS R2 (no covariates): 0.04196 [0.03327, 0.05065]		 age, sex, UKB array type, Genotype PCs —
PPM007314 PSS007130|
European Ancestry|
64,473 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Cholesterol — — R²: 0.07898 [0.07507, 0.08288]
Incremental R2 (full-covars): 0.04327
PGS R2 (no covariates): 0.09873 [0.09445, 0.103]		 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
PSS000662 — — 6,014 individuals — African unspecified — UKB —
PSS000663 — — 1,082 individuals — East Asian — UKB —
PSS000664 — — 23,581 individuals — European Non-British White UKB —
PSS000665 — — 7,336 individuals — South Asian — UKB —
PSS000666 — — 63,794 individuals — European
(British)		 — UKB —
PSS000797 — — 2,129 individuals — European Participants self-identifying as white MESA —
PSS000798 — — 2,004 individuals — European Participants self-identifying as white MESA —
PSS007126 — — 6,097 individuals — African unspecified — UKB —
PSS007127 — — 1,616 individuals — East Asian — UKB —
PSS007128 — — 23,774 individuals — European non-white British ancestry UKB —
PSS007129 — — 7,426 individuals — South Asian — UKB —
PSS007130 — — 64,473 individuals — European white British ancestry UKB Testing cohort (heldout set)