Polygenic Score (PGS) ID: PGS000060

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name GRS_HDL
Development Method
Name Genome-wide significant variants
Parameters p < 5e-8
Variants
Original Genome Build NR
Number of Variants 46
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000045
Citation (link to publication) Johnson L et al. PLoS One (2015)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
99,900 individuals (100%)
PGS Evaluation
African: 25%
Hispanic or Latin American: 25%
East Asian: 25%
European: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000755
Europe PMC: 20686565
 99,900 individuals European NR

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) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000151 PSS000098|
European Ancestry|
2,063 individuals
 PGP000045 |
Johnson L et al. PLoS One (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 PSS000097|
East Asian Ancestry|
666 individuals
 PGP000045 |
Johnson L et al. PLoS One (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 PSS000096|
African Ancestry|
1,355 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum high-density lipoprotein (HDL) levels β: 7.99 — Beta (p-value): 0.00036 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000154 PSS000099|
Hispanic or Latin American Ancestry|
1,256 individuals
 PGP000045 |
Johnson L et al. PLoS One (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

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods 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