Trait: total cholesterol measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004574
Description
  • A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL.
Trait category
Lipid or lipoprotein measurement
Synonyms 2 synonyms
  • cholesterol, total
  • total cholesterol levels
Mapped term(s) SNOMEDCT:121868005

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Number of Variants PGS Scoring File (FTP Link)
PGS000062 GRS_TC PGP000045
Johnson L et al. PLoS One (2015)
total cholesterol 52 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000062/ScoringFiles/PGS000062.txt.gz

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 ID
(PPM ID)
Evaluated Score PGS Sample Set ID
(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
PPM000159 PGS000062 (GRS_TC) PSS000098 PGP000045
Johnson L et al. (2015)
Reported Trait: Serum total cholesterol (TC) levels β: 20.69 Beta (p-value): 0.0108 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000160 PGS000062 (GRS_TC) PSS000097 PGP000045
Johnson L et al. (2015)
Reported Trait: Serum total cholesterol (TC) levels β: 8.57 Beta (p-value): 0.583 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000161 PGS000062 (GRS_TC) PSS000096 PGP000045
Johnson L et al. (2015)
Reported Trait: Serum total cholesterol (TC) levels β: 1.99 Beta (p-value): 0.852 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000162 PGS000062 (GRS_TC) PSS000099 PGP000045
Johnson L et al. (2015)
Reported Trait: Serum total cholesterol (TC) levels β: -2.62 Beta (p-value): 0.815 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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
Mean = 61.5 years 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
Mean = 62.09 years 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
Mean = 60.65 years Hispanic or Latin American MESA MESA Classic Cohort
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,
46.2 % Male samples
Mean = 61.68 years African American or Afro-Caribbean MESA MESA Classic Cohort