Polygenic Score (PGS) ID: PGS004642

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
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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Score Details

Score Construction
PGS Name LDL_EAS_lassosum2
Development Method
Name lassosum2
Parameters Default parameter setting in bigsnpr version 1.12 -- length of tuning parameter path for the the lasso penalty = 30; and regularization parameter for LD matrix is chosen from c(0.001, 0.01, 0.1, 1).
Variants
Original Genome Build GRCh37
Number of Variants 8,643
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)
East Asian: 100%
82,587 individuals (100%)
Score Development/Training
East Asian: 100%
950 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 34887591
 82,587 individuals East 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
— 950 individuals,
32.0 % Male samples
 East Asian UKB — Mean = 52.47 years
Sd = 7.81 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
PPM020827 PSS011426|
East Asian Ancestry|
970 individuals
 PGP000595 |
Zhang J et al. Nat Commun (2024)
 Reported Trait: LDL cholesterol — — adjusted R2: 0.0329 — —

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
PSS011426 — — 970 individuals,
32.0 % Male samples
 Mean = 52.47 years
Sd = 7.81 years		 East Asian — UKB —