Polygenic Score (PGS) ID: PGS003875

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name HDL_PRScsx_ARB_AFRweights
Development Method
Name PRS-CSx
Parameters a=1,b=0.5,phi=0.0001
Variants
Original Genome Build hg19
Number of Variants 1,022,259
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000501
Citation (link to publication) Shim I et al. Nature Communications (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
99,432 individuals (100%)
PGS Evaluation
Greater Middle Eastern: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90239650
Europe PMC: 34887591
 99,432 individuals African American or Afro-Caribbean, African unspecified 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
PPM018767 PSS011097|
Greater Middle Eastern Ancestry|
2,669 individuals
 PGP000501 |
Shim I et al. Nature Communications (2023)
 Reported Trait: HDL cholesterol β: 3.67 (0.27) — R²: 0.1424 age, sex, array version, and the first 10 principal components of ancestry The reported performance was derived from a linearly combined score of 6 normalized ancestry-specific scores using the following coefficients: Score = (0.2431982*zscoreAFR) + (0.8586968*zscoreAMR) + (0.5830709*zscoreARB) + (0.7186383*zscoreEAS) + (1.084247*zscoreEUR) + (1.2259372*zscoreSAS).

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
PSS011097 — — 2,669 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Arab)		 — NR N total after excluding missing values = 2,553