Polygenic Score (PGS) ID: PGS003856

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Sept. 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 PRS59_HDL
Development Method
Name Genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 59
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000493
Citation (link to publication) Li J et al. JAMA Netw Open (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
81,045 individuals (100%)
PGS Evaluation
East Asian: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
Europe PMC: 29083407
47,532 individualsEast Asian12 cohorts
  • CHNS
  • ,CLHNS
  • ,FAMHES
  • ,GBTDS
  • ,NHAPC
  • ,PUUMA
  • ,SBCS
  • ,SIMES
  • ,SMHS
  • ,SP2
  • ,SWHS
  • ,TUDR
GWAS Catalog: GCST003215
Europe PMC: 26582766
8,344 individualsEast AsianNR
GWAS Catalog: GCST004234
Europe PMC: 28334899
25,169 individualsEast AsianNR
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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
PPM018688PSS011066|
East Asian Ancestry|
37,317 individuals
PGP000493 |
Li J et al. JAMA Netw Open (2023)
Reported Trait: Estimated annual change of HDL cholesterol——p-value (inferior to): 0.001——
PPM018692PSS011068|
East Asian Ancestry|
15,664 individuals
PGP000493 |
Li J et al. JAMA Netw Open (2023)
Reported Trait: Estimated annual change of HDL cholesterol——p-value (inferior to): 0.001——
PPM018696PSS011067|
East Asian Ancestry|
21,653 individuals
PGP000493 |
Li J et al. JAMA Netw Open (2023)
Reported Trait: Estimated annual change of HDL cholesterol——p-value (inferior to): 0.001——
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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
PSS011066——37,317 individuals,
41.98 % Male samples
Mean = 51.37 years
Sd = 10.82 years		East Asian—InterASIAChina MUCA, CIMIC
PSS011067——21,653 individuals,
41.98 % Male samples
Mean = 51.22 years
Sd = 10.78 years		East Asian—InterASIAChina MUCA, CIMIC
PSS011068——15,664 individuals,
41.98 % Male samples
Mean = 51.57 years
Sd = 10.87 years		East Asian—InterASIAChina MUCA, CIMIC
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