Polygenic Score (PGS) ID: PGS000064

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name GLGC2017_HDL
Development Method
Name Established Lipid Loci; independent genome-wide significant variants
Parameters MAF < 0.01, Imputation r2 < 0.8, clumping based on r2 > 0.1, overlap of SNPs between study cohorts
Variants
Original Genome Build hg19
Number of Variants 120
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000046
Citation (link to publication) Kuchenbaecker K et al. Nat Commun (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 81.6%
South Asian: 9.2%
African: 5.1%
East Asian: 2.5%
Hispanic or Latin American: 1.5%
331,368 individuals (100%)
PGS Evaluation
European: 60%
African: 20%
East Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 29083408
 17,009 individuals,
33.83 % Male samples
 African unspecified NR
Europe PMC: 29083408
 8,287 individuals,
45.11 % Male samples
 East Asian NR
Europe PMC: 29083408
 270,520 individuals,
46.64 % Male samples
 European NR
Europe PMC: 29083408
 5,084 individuals,
42.68 % Male samples
 Hispanic or Latin American NR
Europe PMC: 29083408
 30,468 individuals,
80.45 % Male samples
 South Asian NR

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
PPM000167 PSS000104|
European Ancestry|
9,962 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 Reported Trait: Serum high-density lipoprotein (HDL) levels — — correlation (r): 0.285 [0.265, 0.305] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000170 PSS000102|
European Ancestry|
1,641 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 Reported Trait: Serum high-density lipoprotein (HDL) levels — — correlation (r): 0.279 [0.222, 0.336] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000173 PSS000103|
European Ancestry|
1,945 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 Reported Trait: Serum high-density lipoprotein (HDL) levels — — correlation (r): 0.268 [0.209, 0.327] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000176 PSS000100|
African Ancestry|
6,407 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 Reported Trait: Serum high-density lipoprotein (HDL) levels — — correlation (r): 0.121 [0.098, 0.145] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000179 PSS000101|
East Asian Ancestry|
21,295 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 Reported Trait: Serum high-density lipoprotein (HDL) levels — — correlation (r): 0.18 [0.145, 0.215] age, sex, region, 20 PCs of genetic ancestry Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA

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
PSS000100 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) — 6,407 individuals,
44.0 % Male samples
 Mean = 34.0 years Sub-Saharan African — APCDR APCDR-Uganda study
PSS000101 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) — 21,295 individuals,
38.0 % Male samples
 Mean = 60.0 years East Asian
(Chinese)		 — CKB - 20810 samples had HDL measurements - 17662 samples had LDL measurements - 20222 samples had triglyceride measurements
PSS000102 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) — 1,641 individuals,
58.0 % Male samples
 Mean = 62.0 years European
(Greek)		 Population isolate from the Pomak villages in the North of Greece HELIC - 1186 samples had HDL measurements - 1186 samples had LDL measurements - 1176 samples had triglyceride measurements
PSS000103 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) — 1,945 individuals,
66.0 % Male samples
 Mean = 45.0 years European
(Greek)		 Population isolate from the Mylopotamos villages in Crete HELIC - 1078 samples had HDL measurements - 1075 samples had LDL measurements - 1066 samples had triglyceride measurements
PSS000104 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) — 9,962 individuals,
56.0 % Male samples
 Mean = 52.0 years European — UKHLS - 9706 samples had HDL measurements - 9767 samples had LDL measurements - 9635 samples had triglyceride measurements