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(Variants and weights)

Polygenic Score (PGS) ID: PGS000062

Predicted Trait

Reported Trait: total cholesterol
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): total cholesterol measurement

Score Details

Name: GRS_TC

Original Genome Build: NR
Number of Variants: 52

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: p < 5e-8

Citation: Johnson L et al. PLoS One (2015) | PGS Catalog Publication ID: PGP000045

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST000760
PubMed: 20686565
100,184 individuals European
(U.K.)

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
PPM000159 PSS000098 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 PSS000097 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 PSS000096 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 PSS000099 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 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