Polygenic Score (PGS) ID: PGS002284

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name GRS_286_HDL
Development Method
Name PRSice
Parameters For GRS construction, SNPs from MVP serum lipid summary statistics were clumped based on their linkage disequilibrium. We clumped SNPs at different r2 thresholds, and a 500kb clumping window with r2 of 0.5 proved to be the best fitting and best performing model for all lipid traits. We also tested the best P-value threshold for selecting which clumped SNPs we would include in the final GRS for the range of 1 to 5E-08. The P-value threshold, which accounted for the highest proportion of the variance of the trait R2, was selected as the best GRS.
Variants
Original Genome Build GRCh38
Number of Variants 286
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000313
Citation (link to publication) Kamiza AB et al. Nat Med (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • African
  • European
  • Hispanic or Latin American
312,571 individuals (100%)
Score Development/Training
African: 100%
6,407 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30275531
312,571 individuals,
92.0 % Male samples
African American or Afro-Caribbean, European, Hispanic or Latin American MVP
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 31675503
6,407 individuals,
26.2 % Male samples
Sub-Saharan African
(Ugandans)
UGR Non-fasting serum lipid levels were measured using the Cobas Integra 400 Plus Chemistry analyser, an automated analyser that employs four different technologies: absorption photometry, fluorescence polarization immunoassay, immune-turbidimetry, and potentiometry for accurate analysis. LDL-C were measured using the homogeneous enzymatic colorimetric assays Mean = 34.1 years
Ci = [15.8, 52.4] years

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
PPM012982 PSS009639|
African Ancestry|
2,569 individuals
PGP000313 |
Kamiza AB et al. Nat Med (2022)
Reported Trait: High density lipoprotein cholesterol levels : 0.0213 age, sex, type 2 diabetes, PC1, PC2, PC3, PC4, PC5 Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment)

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
PSS009639 Non-fasting serum lipid levels were measured using the Cobas Integra 400 Plus Chemistry analyser, an automated analyser that employs four different technologies: absorption photometry, fluorescence polarization immunoassay, immune-turbidimetry, and potentiometry for accurate analysis. LDL-C were measured using the homogeneous enzymatic colorimetric assays 2,569 individuals,
42.9 % Male samples
Mean = 33.1 years
Ci = [18.0, 48.2] years
Sub-Saharan African
(South Africans)
SAZ