Polygenic Score (PGS) ID: PGS000688

Predicted Trait
Reported Trait LDL cholesterol [mmol/L] (statin adjusted)
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
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.LDL_direct_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 16,184
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
PPM001416 PSS000714|
African Ancestry|
6,003 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — R²: 0.13357
Spearman's ρ: 0.289		 Age, sex, PCs(1-40) —
PPM001451 PSS000715|
East Asian Ancestry|
1,082 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — R²: 0.13985
Spearman's ρ: 0.301		 Age, sex, PCs(1-40) —
PPM001486 PSS000716|
European Ancestry|
23,535 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — R²: 0.26408
Spearman's ρ: 0.436		 Age, sex, PCs(1-40) —
PPM001521 PSS000717|
South Asian Ancestry|
7,319 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — R²: 0.11217
Spearman's ρ: 0.289		 Age, sex, PCs(1-40) —
PPM001556 PSS000718|
European Ancestry|
63,675 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — R²: 0.26409
Spearman's ρ: 0.446		 Age, sex, PCs(1-40) —
PPM001575 PSS000824|
European Ancestry|
2,097 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — Spearman's ρ: 0.159 Age, sex —
PPM001576 PSS000825|
European Ancestry|
1,987 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: LDL cholesterol [mmol/L] (statin adjusted) — — Spearman's ρ: 0.138 Age, sex —
PPM007365 PSS007171|
African Ancestry|
6,086 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: LDL cholesterol — — R²: 0.05912 [0.048, 0.07024]
Incremental R2 (full-covars): 0.05479
PGS R2 (no covariates): 0.06663 [0.05492, 0.07834]		 age, sex, UKB array type, Genotype PCs —
PPM007366 PSS007172|
East Asian Ancestry|
1,615 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: LDL cholesterol — — R²: 0.06107 [0.03908, 0.08305]
Incremental R2 (full-covars): 0.0498
PGS R2 (no covariates): 0.07486 [0.05087, 0.09885]		 age, sex, UKB array type, Genotype PCs —
PPM007367 PSS007173|
European Ancestry|
23,728 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: LDL cholesterol — — R²: 0.10564 [0.09842, 0.11286]
Incremental R2 (full-covars): 0.096
PGS R2 (no covariates): 0.11974 [0.11218, 0.12731]		 age, sex, UKB array type, Genotype PCs —
PPM007368 PSS007174|
South Asian Ancestry|
7,407 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: LDL cholesterol — — R²: 0.05634 [0.04642, 0.06625]
Incremental R2 (full-covars): 0.02423
PGS R2 (no covariates): 0.03502 [0.02702, 0.04301]		 age, sex, UKB array type, Genotype PCs —
PPM007369 PSS007175|
European Ancestry|
64,356 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: LDL cholesterol — — R²: 0.09533 [0.09111, 0.09955]
Incremental R2 (full-covars): 0.08543
PGS R2 (no covariates): 0.10869 [0.10426, 0.11313]		 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
PSS000714 — — 6,003 individuals — African unspecified — UKB —
PSS000715 — — 1,082 individuals — East Asian — UKB —
PSS000716 — — 23,535 individuals — European Non-British White UKB —
PSS000717 — — 7,319 individuals — South Asian — UKB —
PSS000718 — — 63,675 individuals — European
(British)		 — UKB —
PSS007171 — — 6,086 individuals — African unspecified — UKB —
PSS007172 — — 1,615 individuals — East Asian — UKB —
PSS007173 — — 23,728 individuals — European non-white British ancestry UKB —
PSS007174 — — 7,407 individuals — South Asian — UKB —
PSS007175 — — 64,356 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000824 — — 2,097 individuals — European Participants self-identifying as white MESA —
PSS000825 — — 1,987 individuals — European Participants self-identifying as white MESA —