Polygenic Score (PGS) ID: PGS003879

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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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_PRScsx_ARB_EURweights
Development Method
Name PRS-CSx
Parameters a=1,b=0.5,phi=0.0001
Variants
Original Genome Build hg19
Number of Variants 1,069,677
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)
European: 100%
1,320,016 individuals (100%)
PGS Evaluation
Greater Middle Eastern: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST90239652
Europe PMC: 34887591
1,320,016 individualsEuropeanNR
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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
PPM018771PSS011097|
Greater Middle Eastern Ancestry|
2,669 individuals
PGP000501 |
Shim I et al. Nature Communications (2023)
Reported Trait: HDL cholesterolβ: 3.67 (0.27)—R²: 0.1424age, sex, array version, and the first 10 principal components of ancestryThe reported performance was derived from a linearly combined score of 6 normalized ancestry-specifi... c scores using the following coefficients: Score = (0.2431982*zscoreAFR) + (0.8586968*zscoreAMR) + (0.5830709*zscoreARB) + (0.7186383*zscoreEAS) + (1.084247*zscoreEUR) + (1.2259372*zscoreSAS).Show more
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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
PSS011097——2,669 individuals—Greater Middle Eastern (Middle Eastern, North African or Persian)
(Arab)		—NRN total after excluding missing values = 2,553
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