Polygenic Score (PGS) ID: PGS005396

Predicted Trait
Reported Trait Breast carcinoma
Mapped Trait(s) breast carcinoma (MONDO_0004989)
Released in PGS Catalog: July 15, 2026
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Score Details

Score Construction
PGS Name AFR_BCa_PRS_CSx
Development Method
Name PRS-CSx
Parameters Trained using PRS-CSx (single-population mode) with African ancestry LD reference (1000 Genomes). Parameters: a=1, b=0.5, phi=auto.
Variants
Original Genome Build GRCh37
Number of Variants 139,306
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000779
Citation (link to publication) David E et al. medRxiv (2026) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 59.1%
African: 30%
Hispanic or Latin American: 10.9%
55,309 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90479801
Europe PMC: 39024449
 16,586 individuals African American or Afro-Caribbean MVP
GWAS Catalog: GCST90479801
Europe PMC: 39024449
 32,714 individuals European MVP
GWAS Catalog: GCST90479801
Europe PMC: 39024449
 6,009 individuals Hispanic or Latin American 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
PPM023439 PSS012182|
African Ancestry|
1,565 individuals
 PGP000779 |
David E et al. medRxiv (2026)
|Pre		 Reported Trait: Breast carcinoma OR: 1.11 AUROC: 0.77 Nagelkerke Delta R2: 0.0018 age, sex OR per Standard Deviation

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
PSS012182 ICD-10 codes for malignant neoplasm of breast —
[
  • 166 cases
  • , 1,399 controls
]
 — Sub-Saharan African
(African/African-admixed)		 — UKB —