Polygenic Score (PGS) ID: PGS000686

Predicted Trait
Reported Trait HDL cholesterol [mmol/L]
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
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.HDL_cholesterol
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 25,069
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
PPM001519 PSS000702|
South Asian Ancestry|
6,689 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — Spearman's ρ: 0.39
R²: 0.30375		 Age, sex, PCs(1-40) —
PPM001554 PSS000703|
European Ancestry|
58,251 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — R²: 0.35648
Spearman's ρ: 0.438		 Age, sex, PCs(1-40) —
PPM001577 PSS000818|
European Ancestry|
2,127 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — Spearman's ρ: 0.301 Age, sex —
PPM001578 PSS000819|
European Ancestry|
2,002 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — Spearman's ρ: 0.305 Age, sex —
PPM001414 PSS000699|
African Ancestry|
5,573 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — R²: 0.17487
Spearman's ρ: 0.241		 Age, sex, PCs(1-40) —
PPM001449 PSS000700|
East Asian Ancestry|
986 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — R²: 0.31466
Spearman's ρ: 0.326		 Age, sex, PCs(1-40) —
PPM001484 PSS000701|
European Ancestry|
21,542 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HDL cholesterol [mmol/L] — — R²: 0.36109
Spearman's ρ: 0.422		 Age, sex, PCs(1-40) —
PPM007355 PSS007161|
African Ancestry|
5,656 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: HDL cholesterol — — R²: 0.17012 [0.15349, 0.18676]
Incremental R2 (full-covars): 0.05232
PGS R2 (no covariates): 0.05099 [0.04058, 0.06141]		 age, sex, UKB array type, Genotype PCs —
PPM007356 PSS007162|
East Asian Ancestry|
1,475 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: HDL cholesterol — — R²: 0.29075 [0.25451, 0.32699]
Incremental R2 (full-covars): 0.07379
PGS R2 (no covariates): 0.07936 [0.05478, 0.10393]		 age, sex, UKB array type, Genotype PCs —
PPM007357 PSS007163|
European Ancestry|
21,750 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: HDL cholesterol — — R²: 0.32462 [0.31507, 0.33418]
Incremental R2 (full-covars): 0.13703
PGS R2 (no covariates): 0.14659 [0.13848, 0.15471]		 age, sex, UKB array type, Genotype PCs —
PPM007358 PSS007164|
South Asian Ancestry|
6,782 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: HDL cholesterol — — R²: 0.27847 [0.26161, 0.29532]
Incremental R2 (full-covars): 0.12939
PGS R2 (no covariates): 0.13685 [0.12272, 0.15099]		 age, sex, UKB array type, Genotype PCs —
PPM007359 PSS007165|
European Ancestry|
59,060 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: HDL cholesterol — — R²: 0.32153 [0.31572, 0.32734]
Incremental R2 (full-covars): 0.14881
PGS R2 (no covariates): 0.16158 [0.15649, 0.16667]		 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
PSS007164 — — 6,782 individuals — South Asian — UKB —
PSS007165 — — 59,060 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000818 — — 2,127 individuals — European Participants self-identifying as white MESA —
PSS000819 — — 2,002 individuals — European Participants self-identifying as white MESA —
PSS000699 — — 5,573 individuals — African unspecified — UKB —
PSS000700 — — 986 individuals — East Asian — UKB —
PSS000701 — — 21,542 individuals — European Non-British White UKB —
PSS000702 — — 6,689 individuals — South Asian — UKB —
PSS000703 — — 58,251 individuals — European
(British)		 — UKB —
PSS007161 — — 5,656 individuals — African unspecified — UKB —
PSS007162 — — 1,475 individuals — East Asian — UKB —
PSS007163 — — 21,750 individuals — European non-white British ancestry UKB —