Polygenic Score (PGS) ID: PGS004624

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Additional Trait Information Phenotype defined in GLGC. Please refer the paper for more details.
Released in PGS Catalog: April 18, 2024
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name HDL_AFR_PROSPER
Development Method
Name PROSPER
Parameters Default parameter setting in PROSPER package from GitHub (https://github.com/Jingning-Zhang/PROSPER) -- Ll =5, Lc=5.
Variants
Original Genome Build GRCh37
Number of Variants 1,688,569
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000595
Citation (link to publication) Zhang J et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • African
  • Hispanic or Latin American
  • East Asian
  • South Asian
1,179,560 individuals (100%)
Score Development/Training
African: 100%
3,971 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: 34887591
 1,179,560 individuals European, African American or Afro-Caribbean, Hispanic or Latin American, East Asian, South Asian GLGC
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
— 3,971 individuals,
42.0 % Male samples
 African American or Afro-Caribbean
(African American)		 UKB — Mean = 51.82 years
Sd = 8.06 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
PPM020809 PSS011419|
African Ancestry|
3,983 individuals
 PGP000595 |
Zhang J et al. Nat Commun (2024)
 Reported Trait: HDL cholesterol — — adjusted R2: 0.1096 — —

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
PSS011419 — — 3,983 individuals,
42.0 % Male samples
 Mean = 51.82 years
Sd = 8.06 years		 African American or Afro-Caribbean — UKB —