Polygenic Score (PGS) ID: PGS004126

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Dec. 19, 2023
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Score Details

Score Construction
PGS Name pt_clump_nested.CV.GCST007140.HDL
Development Method
Name pt_clump_nested.CV
Parameters p0.000001, r2 = 0.1, window = 250kb
Variants
Original Genome Build GRCh38
Number of Variants 579
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 87.3%
Hispanic or Latin American: 8.9%
African: 3.4%
South Asian: 0.5%
87,819 individuals (100%)
Score Development/Training
European: 100%
315,135 individuals (100%)
PGS Evaluation
European: 60%
South Asian: 40%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007140
Europe PMC: 29507422
 76,627 individuals European NR
GWAS Catalog: GCST007140
Europe PMC: 29507422
 7,795 individuals Hispanic or Latin American NR
GWAS Catalog: GCST007140
Europe PMC: 29507422
 2,958 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST007140
Europe PMC: 29507422
 439 individuals South Asian NR
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
— 315,135 individuals European UKB — — — — —

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
PPM019591 PSS011218|
European Ancestry|
10,642 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: high-density lipoprotein cholesterol β: 0.20542 [0.18681969, 0.22401137] — R²: 0.0422 [0.0349016, 0.05018109] 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019592 PSS011241|
South Asian Ancestry|
29,628 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: high-density lipoprotein cholesterol β: 0.26646 [0.25548665, 0.27743738] — R²: 0.071 [0.06527343, 0.0769715] 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019593 PSS011257|
European Ancestry|
49,824 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: high-density lipoprotein cholesterol β: 0.25473 [0.24623963, 0.26322204] — R²: 0.06489 [0.06063396, 0.06928584] 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019594 PSS011285|
South Asian Ancestry|
8,065 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: high-density lipoprotein cholesterol β: 0.22475 [0.20348197, 0.2460197] — R²: 0.05051 [0.04140491, 0.06052569] 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019595 PSS011271|
European Ancestry|
78,782 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: high-density lipoprotein cholesterol β: 0.2406 [0.23382893, 0.24736942] — R²: 0.05801 [0.05479162, 0.06132106] 0 beta = sd_trait/sd_pgs = pearson correlation

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
PSS011271 — — 78,782 individuals — European — UKB —
PSS011241 — — 29,628 individuals — South Asian — G&H —
PSS011218 — — 10,642 individuals — European — EB —
PSS011285 — — 8,065 individuals — South Asian — UKB —
PSS011257 — — 49,824 individuals — European — HUNT —