Polygenic Score (PGS) ID: PGS004938

Predicted Trait
Reported Trait Severe COVID-19 course
Mapped Trait(s) COVID-19 (MONDO_0100096)
Released in PGS Catalog: Oct. 8, 2024
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Score Details

Score Construction
PGS Name pgs_data_ldpred
Development Method
Name Ldpred2
Parameters r2=0.021, p=0.01000, h2=0.8035
Variants
Original Genome Build GRCh37
Number of Variants 955,503
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000666
Citation (link to publication) Kovalenko E et al. Front Med (Lausanne) (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 87.6%
African: 4.6%
Hispanic or Latin American: 4%
South Asian: 1.9%
East Asian: 1.3%
Greater Middle Eastern: 0.6%
Not Reported: 0.01%
3,225,764 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 11,419 cases
  • , 137,472 controls
]
 African unspecified NR
[
  • 22,522 cases
  • , 107,107 controls
]
 Hispanic or Latin American NR
[
  • 4,459 cases
  • , 36,121 controls
]
 East Asian NR
[
  • 171,885 cases
  • , 2,653,285 controls
]
 European NR
[
  • 3,539 cases
  • , 15,274 controls
]
 Greater Middle Eastern (Middle Eastern, North African or Persian) NR
[
  • 175 cases
  • , 160 controls
]
 Not reported NR
[
  • 9,860 cases
  • , 52,486 controls
]
 South Asian NR

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
PPM021730 PSS011763|
European Ancestry|
7,124 individuals
 PGP000666 |
Kovalenko E et al. Front Med (Lausanne) (2024)
 Reported Trait: Severe COVID-19 course — AUROC: 0.6 Odds ratio (OR, high vs low tertile): 2.25 PC1-20, sex, gender —

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
PSS011763 Very severe respiratory confirmed covid vs. not severe respiratory confirmed covid —
[
  • 724 cases
  • , 6,400 controls
]
 — European — Genotek —