Polygenic Score (PGS) ID: PGS004895

Predicted Trait
Reported Trait Estrogen receptor negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: May 8, 2024
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Score Details

Score Construction
PGS Name ERneg.prs
Development Method
Name Thresholding Stepwise Forward Logistic Regression
Parameters LD r2 < 0.9, p value <0.05
Original Genome Build hg19
Number of Variants 28,405
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000621
Citation (link to publication) Gao G et al. Hum Mol Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 92.1%
African: 7.9%
172,246 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30554720
  • 88,916 cases
  • , 69,732 controls
European BCAC
  • 6,533 cases
  • , 7,065 controls
African American or Afro-Caribbean
(African American, African, and African Barbadian)

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM021275 PSS011673|
African Ancestry|
5,821 individuals
PGP000621 |
Gao G et al. Hum Mol Genet (2022)
Reported Trait: Estrogen receptor negative breast cancer OR: 1.31 [1.21, 1.43] AUROC: 0.576 [0.553, 0.598] age, consortium/study, and top 10 principal components

Evaluated Samples

PGS Sample Set ID
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
  • 2,702 cases
  • , 3,119 controls
Mean = 52.7 years
Sd = 12.7 years
African American or Afro-Caribbean
(African American, African, and African Barbadian)