Polygenic Score (PGS) ID: PGS004633

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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Terms and Licenses
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_SAS_ldpred2
Development Method
Name ldpred2
Parameters Default parameter setting in bigsnpr version 1.12 -- the proportion of causal SNPs is chosen from a sequence of length 17 that are evenly spaced on a logarithmic scale from 10^(-4) to 1; per-SNP heritability is chosen from 0.7, 1, or 1.4 times the total heritability estimated by LD score regression divided by the number of causal SNPs. "sparse” option = to FALSE.
Variants
Original Genome Build GRCh37
Number of Variants 1,476,939
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)
South Asian: 100%
33,953 individuals (100%)
Score Development/Training
South Asian: 100%
4,683 individuals (100%)
PGS Evaluation
South Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 34887591
 33,953 individuals 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
— 4,683 individuals,
53.0 % Male samples
 South Asian UKB — Mean = 53.37 years
Sd = 8.43 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
PPM020818 PSS011427|
South Asian Ancestry|
4,702 individuals
 PGP000595 |
Zhang J et al. Nat Commun (2024)
 Reported Trait: HDL cholesterol — — adjusted R2: 0.1016 — —

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
PSS011427 — — 4,702 individuals,
53.0 % Male samples
 Mean = 53.37 years
Sd = 8.43 years		 South Asian — UKB —