Trait: high density lipoprotein cholesterol measurement

Information

Experimental Factor Ontology ID: EFO_0004612

EFO Trait Description:

  • The measurement of HDL cholesterol in blood used as a risk indicator for heart disease.

Associated PGS

PGS 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 Evaluated Score 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
PPM000151 PGS000060 (GRS_HDL) PSS000098 Johnson L et al. (2015) Reported Trait: Serum high-density lipoprotein (HDL) levels β: 8.39 Beta (p-value): 2.76e-06 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000152 PGS000060 (GRS_HDL) PSS000097 Johnson L et al. (2015) Reported Trait: Serum high-density lipoprotein (HDL) levels β: 15.58 Beta (p-value): 2.17e-07 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000153 PGS000060 (GRS_HDL) PSS000096 Johnson L et al. (2015) Reported Trait: Serum high-density lipoprotein (HDL) levels β: 7.99 Beta (p-value): 0.000364 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000154 PGS000060 (GRS_HDL) PSS000099 Johnson L et al. (2015) Reported Trait: Serum high-density lipoprotein (HDL) levels β: 10.97 Beta (p-value): 6.48e-10 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000167 PGS000064 (GLGC2017_HDL) PSS000104 Kuchenbaecker K et al. (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 PGS000064 (GLGC2017_HDL) PSS000102 Kuchenbaecker K et al. (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 PGS000064 (GLGC2017_HDL) PSS000103 Kuchenbaecker K et al. (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 PGS000064 (GLGC2017_HDL) PSS000100 Kuchenbaecker K et al. (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 PGS000064 (GLGC2017_HDL) PSS000101 Kuchenbaecker K et al. (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 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
PSS000096 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. 1,355 individuals
46.20 % Male samples
African American or Afro-Caribbean MESA MESA Classic Cohort
PSS000097 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. 666 individuals
50.15 % Male samples
East Asian MESA MESA Classic Cohort
PSS000098 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. 2,063 individuals
46.78 % Male samples
European MESA MESA Classic Cohort
PSS000099 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. 1,256 individuals
48.89 % Male samples
Hispanic or Latin American MESA MESA Classic Cohort
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