Polygenic Score (PGS) ID: PGS000061

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Predicted Trait
Reported Trait low-density lipoprotein (LDL) cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name GRS_LDL
Variants
Original Genome Build NR
Number of Variants 37
Development Method
Name Genome-wide significant SNPs
Parameters p < 5e-8
PGS Source
PGS Catalog Publication (PGP) ID PGP000045
Citation (link to publication) Johnson L et al. PLoS One (2015)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST000759
EuropePMC: 20686565		 95,454 individuals European

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) 		PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000158 PSS000099 PGP000045
Johnson L et al. (2015) 		Reported Trait: Serum low-density lipoprotein (LDL) levels β: 42.86 — Beta (p-value): 1.94e-05 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000157 PSS000096 PGP000045
Johnson L et al. (2015) 		Reported Trait: Serum low-density lipoprotein (LDL) levels β: 30.04 — Beta (p-value): 0.00282 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000156 PSS000097 PGP000045
Johnson L et al. (2015) 		Reported Trait: Serum low-density lipoprotein (LDL) levels β: 5.58 — Beta (p-value): 0.697 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000155 PSS000098 PGP000045
Johnson L et al. (2015) 		Reported Trait: Serum low-density lipoprotein (LDL) levels β: 15.0 — Beta (p-value): 0.0352 age, age^2, sex, GRS_HDL, GRS_TC, 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