Polygenic Score (PGS) ID: PGS005049

Predicted Trait
Reported Trait Angina pectoris (PheCode 411.3)
Mapped Trait(s) angina pectoris (EFO_0003913)
Released in PGS Catalog: Oct. 8, 2024
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Score Details

Score Construction
PGS Name Phe_411_3_ldpred_HISss_amrld
Development Method
Name ldpred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,286,612
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000679
Citation (link to publication) Gunn S et al. HGG Adv (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Not Reported: 50.3%
European: 36.1%
African: 9.5%
Hispanic or Latin American: 4.1%
1,192,350 individuals (100%)
PGS Evaluation
African: 33.3%
Hispanic or Latin American: 33.3%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 7,516 cases
  • , 106,211 controls
]
 African American or Afro-Caribbean MVP
—
[
  • 37,853 cases
  • , 392,239 controls
]
 European MVP
—
[
  • 3,211 cases
  • , 45,239 controls
]
 Hispanic or Latin American MVP
—
[
  • 48,939 cases
  • , 551,142 controls
]
 Not reported MVP

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
PPM021927 PSS011819|
European Ancestry|
30,750 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: Angina pectoris OR: 1.115 [1.07, 1.17] C-index: 0.75404 — age, sex, 20 PCs —
PPM021921 PSS011809|
Hispanic or Latin American Ancestry|
8,114 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: Angina pectoris OR: 1.17 [1.04, 1.32] C-index: 0.7981 — age, sex, 20 PCs —
PPM021933 PSS011799|
African Ancestry|
10,445 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: Angina pectoris OR: 1.102 [0.99, 1.22] C-index: 0.74684 — age, sex, 20 PCs —

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
PSS011809 — —
[
  • 371 cases
  • , 7,743 controls
]
 — Hispanic or Latin American — AllofUs —
PSS011819 — —
[
  • 2,154 cases
  • , 28,596 controls
]
 — European — AllofUs —
PSS011799 — —
[
  • 505 cases
  • , 9,940 controls
]
 — African American or Afro-Caribbean — AllofUs —