Polygenic Score (PGS) ID: PGS005106

Predicted Trait
Reported Trait ER-negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: Dec. 16, 2024
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Score Details

Score Construction
PGS Name PRSAFR_ER−
Development Method
Name Genome-wide significant SNPs
Parameters MAF > 0.01, r2 > 0.8
Variants
Original Genome Build NR
Number of Variants 24
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000694
Citation (link to publication) Jia G et al. Nat Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
21,982 individuals (100%)
Score Development/Training
African: 100%
33,042 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: GCST90296721
Europe PMC: 38741014
 21,982 individuals African American or Afro-Caribbean, Sub-Saharan African, African unspecified WAABCS
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 15,680 cases
  • , 17,362 controls
]
,
0.0 % Male samples
 African American or Afro-Caribbean 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
PPM022288 PSS011900|
African Ancestry|
4,814 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
 Reported Trait: ER-negative breast cancer OR: 1.67 [1.49, 1.87] AUROC: 0.62 [0.59, 0.66] — — —

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
PSS011900 — —
[
  • 617 cases
  • , 4,197 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — AABCG —