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(Variants and weights)

Polygenic Score (PGS) ID: PGS000065

Predicted Trait

Reported Trait: Low density lipoprotein (HDL) cholesterol
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): low density lipoprotein cholesterol measurement

Score Details

Name: GLGC2017_LDL

Original Genome Build: hg19
Number of Variants: 103

PGS Development Method: Established Lipid Loci; independent genome-wide significant variants
PGS Development Details/Relevant Parameters: MAF < 0.01, Imputation r2 < 0.8, clumping based on r2 > 0.1, overlap of SNPs between study cohorts

Citation: Kuchenbaecker K et al. Nat Commun (2019) | PGS Catalog Publication ID: PGP000046

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
PubMed: 29083408.0 17,009 individuals
33.83 % Male samples
African unspecified
PubMed: 29083408.0 8,287 individuals
45.11 % Male samples
East Asian
PubMed: 29083408.0 270,520 individuals
46.64 % Male samples
European
PubMed: 29083408.0 5,084 individuals
42.68 % Male samples
Hispanic or Latin American
PubMed: 29083408.0 30,468 individuals
80.45 % Male samples
South Asian

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000168 PSS000104 Kuchenbaecker K et al. (2019) Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.274 [0.254 - 0.294] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000171 PSS000102 Kuchenbaecker K et al. (2019) Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.229 [0.172 - 0.286] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000174 PSS000103 Kuchenbaecker K et al. (2019) Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.29 [0.231 - 0.349] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000177 PSS000100 Kuchenbaecker K et al. (2019) Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.28 [0.257 - 0.304] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000180 PSS000101 Kuchenbaecker K et al. (2019) Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.198 [0.161 - 0.235] 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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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
44.00 % Male samples
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
38.00 % Male samples
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
58.00 % Male samples
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
66.00 % Male samples
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
56.00 % Male samples
European UKHLS - 9706 samples had HDL measurements - 9767 samples had LDL measurements - 9635 samples had triglyceride measurements