Polygenic Score (PGS) ID: PGS004677

Predicted Trait
Reported Trait Total cholesterol
Mapped Trait(s) total cholesterol measurement (EFO_0004574)
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 TC_SAS_lassosum2
Development Method
Name lassosum2
Parameters Default parameter setting in bigsnpr version 1.12 -- length of tuning parameter path for the the la... sso penalty = 30; and regularization parameter for LD matrix is chosen from c(0.001, 0.01, 0.1, 1).Show more
Variants
Original Genome Build GRCh37
Number of Variants 2,421
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%
34,135 individuals (100%)
Score Development/Training
South Asian: 100%
5,147 individuals (100%)
PGS Evaluation
South Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
Europe PMC: 34887591
34,135 individualsSouth AsianGLGC
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Score Development/Training
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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
—5,147 individuals,
53.0 % Male samples
South AsianUKB—Mean = 53.37 years
Sd = 8.43 years		———
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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.

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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
PPM020862PSS011429|
South Asian Ancestry|
5,153 individuals
PGP000595 |
Zhang J et al. Nat Commun (2024)
Reported Trait: Total cholesterol——adjusted R2: 0.0282——
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Evaluated Samples

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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
PSS011429——5,153 individuals,
53.0 % Male samples
Mean = 53.37 years
Sd = 8.43 years		South Asian—UKB—
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