Polygenic Score (PGS) ID: PGS000192

Predicted Trait
Reported Trait Cholesterol
Mapped Trait(s)
Released in PGS Catalog: May 20, 2020
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Score Details

Score Construction
PGS Name GS9
Variants
Original Genome Build NCBI35
Number of Variants 9
Development Method
Name Curated variant associations
Parameters Correlated SNPs were pruned from the score
PGS Source
PGS Catalog Publication (PGP) ID PGP000079
Citation (link to publication) Kathiresan S et al. N Engl J Med (2008)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 47.7%
Not Reported: 44.4%
African: 5.9%
Hispanic or Latin American: 2%
30,795 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
9,185 individuals European
Europe PMC: 10.1086/500615
1,822 individuals African American or Afro-Caribbean
Europe PMC: 10.1086/500615
1,045 individuals European
Europe PMC: 10.1086/500615
601 individuals Hispanic or Latin American
13,677 individuals NR
1,465 individuals European
3,000 individuals European

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
PPM000563 PSS000292|
European Ancestry|
4,232 individuals
PGP000079 |
Kathiresan S et al. N Engl J Med (2008)
Reported Trait: Incident cardiovascular event AUROC: 0.8 Hazard Ratio (HR; per allele): 1.15 [1.07, 1.24] age, sex, family history of MI, LDL cholesterol, HDL cholesterol, triglycerides, blood pressure, body mass index, diabetes status, smoking status, CRP, lipid lowering medication
PPM000562 PSS000292|
European Ancestry|
4,232 individuals
PGP000079 |
Kathiresan S et al. N Engl J Med (2008)
Reported Trait: High-density lipoprotein (HDL) levels Association p-value: 2.00e-18
PPM000561 PSS000292|
European Ancestry|
4,232 individuals
PGP000079 |
Kathiresan S et al. N Engl J Med (2008)
Reported Trait: Low-density lipoprotein (LDL) levels Association p-value: 3.00e-24

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
PSS000292 Composite end point of cardiovascular events was defined as myocardial infarction, ischemic stroke, and death from coronary heart disease. Death from coronary heart disease was defined on the basis of codes 412 and 414 (ICD-9) or I22–I23 and I25 (ICD-10) in the Swedish Cause of Death Register. Myocardial infarction was defined on the basis of codes 410 and I21 in the International Classification of Diseases, 9th Revision and 10th Revision (ICD-9 and ICD-10), respectively. Ischemic stroke was defined on the basis of codes 434 or 436 (ICD-9) and I63 or I64 (ICD-10). Median = 10.6 years
[
  • 238 cases
  • , 3,994 controls
]
European MDC