Polygenic Score (PGS) ID: PGS005382

Predicted Trait
Reported Trait Estrogen-receptor negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: Feb. 26, 2026
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Terms and Licenses
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Score Details

Score Construction
PGS Name Erneg_M1
Development Method
Name Ensemble-based approach
Parameters LD r2 < 0.9, Ensemble-based PRS models by incorporating all PRS models generated across phenotypes using elastic net method in the tuning set, and existing European 313-/330-variant models
Variants
Original Genome Build hg38
Number of Variants 2,005,141
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000774
Citation (link to publication) Li JL et al. Nat Genet (2026)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
25,334 individuals (100%)
Score Development/Training
African: 100%
28,953 individuals (100%)
PGS Evaluation
African: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 12,174 cases
  • , 13,160 controls
]
,
0.0 % Male samples
 African American or Afro-Caribbean
(African)		 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
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
—
[
  • 13,913 cases
  • , 15,040 controls
]
,
0.0 % Male samples
 African American or Afro-Caribbean
(African)		 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 — — — — —

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
PPM023408 PSS012171|
African Ancestry|
4,677 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor nagetive breast cancer risk OR: 1.49 [1.38, 1.61] AUROC: 0.611 [0.591, 0.632] — — —
PPM023420 PSS012172|
African Ancestry|
6,458 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor nagetive breast cancer risk — AUROC: 0.605 [0.555, 0.657] — — —

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
PSS012172 — —
[
  • 281 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012172 — —
[
  • 155 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012171 — —
[
  • 917 cases
  • , 3,760 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 —