Polygenic Score (PGS) ID: PGS000825

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Additional Trait Information EFO:0004612
Released in PGS Catalog: July 29, 2021
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Terms and Licenses
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)

Score Details

Score Construction
PGS Name HDL-C_PGS
Development Method
Name Pruning of FDR filtered SNPs
Parameters FDR < 5%, r^2 < 0.2
Variants
Original Genome Build hg19
Number of Variants 883
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000210
Citation (link to publication) Zubair N et al. Sci Rep (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
94,595 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • Additional Asian Ancestries
  • Hispanic or Latin American
  • African
  • Not Reported
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002223
Europe PMC: 24097068
 94,595 individuals European 23 cohorts
  • AGES
  • ,ARIC
  • ,B58C
  • ,BLSA
  • ,BRIGHT
  • ,CHS
  • ,CoLaus
  • ,DGI
  • ,EPIC-Norfolk
  • ,FHS
  • ,FINRISK
  • ,FUSION
  • ,Fenland
  • ,GENMETS
  • ,GenomEUtwin
  • ,InCHIANTI
  • ,KORA
  • ,LOLIPOP
  • ,MedSTAR
  • ,NFBC
  • ,PennCATH
  • ,RS
  • ,SUVIMAX

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
PPM002231 PSS001083|
Multi-ancestry (including European)|
2,531 individuals
 PGP000210 |
Zubair N et al. Sci Rep (2019)
 Reported Trait: High density lipoprotein cholesterol — — R²: 0.069 Age at baseline, sex, enrollment channel, PCs(1-7), observation season, observation vendor —

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
PSS001083 Of the 2,531 participants, 1,809 had longitudinal observations for total cholesterol (mg/dL), high density lipoprotein cholesterol (mg/dL) and trigycerides (mg/dL), 1,801 had longitudinal observations for low density lipoprotein cholesterol (mg/dL), 1,325 had longitudinal observations for waist circumference (inches), 2,355 had longitudinal observations for body mass index (kg/m^2) and 1,572 had longitudinal observations for homocysteine (μmol/L). — 2,531 individuals,
40.0 % Male samples
 Mean = 48.0 years
Sd = 12.0 years		 European, Asian unspecified, Hispanic or Latin American, African unspecified, NR European = 1,999, Asian unspecified = 228, Hispanic or Latin American = 101, African unspecified = 51, Not reported = 152 NR Participants were obtained from the Scientific Wellness Program.