Polygenic Score (PGS) ID: PGS002781

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Dec. 6, 2022
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Score Details

Score Construction
PGS Name GLGC_2021_ALL_HDL_PRS_weights_PRS-CS
Development Method
Name PRS-CS
Parameters 1000Genomes reference panel
Variants
Original Genome Build hg19
Number of Variants 1,239,184
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000366
Citation (link to publication) Kanoni S et al. Genome Biol (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 79.8%
East Asian: 8.9%
African: 6%
Hispanic or Latin American: 2.9%
South Asian: 2.5%
1,654,960 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • African
  • East Asian
  • South Asian
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90239649
Europe PMC: 34887591
 40,963 individuals South Asian NR
GWAS Catalog: GCST90239649
Europe PMC: 34887591
 48,057 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90239649
Europe PMC: 34887591
 99,432 individuals African American or Afro-Caribbean,African unspecified NR
GWAS Catalog: GCST90239649
Europe PMC: 34887591
 146,492 individuals East Asian NR
GWAS Catalog: GCST90239649
Europe PMC: 34887591
 1,320,016 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
PPM016161 PSS010052|
Multi-ancestry (including European)|
461,918 individuals
 PGP000366 |
Kanoni S et al. Genome Biol (2022)
 Reported Trait: Baseline HDL cholesterol — — R²: 0.13 sex, batch, age at initial assessment, PCs1-4 —

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
PSS010052 — — 461,918 individuals — European, African unspecified, East Asian, South Asian — UKB —