Polygenic Score (PGS) ID: PGS005378

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Feb. 26, 2026
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Terms and Licenses
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Score Details

Score Construction
PGS Name Overall_Prop_M1
Development Method
Name forward stepwise selection (FSS), PRSice-2, elastic net (EN)
Parameters LD r2 < 0.9, FSS p <0.05, PRSice-2 with optimally selected p-value threshold between 5x10-8 and 0.5 (increments of 5x10-5) that offered the maximum r2 value when regressing each BC phenotype on the selected PRS, EN optimal lambda by minimazing prediction error using 10-fold cross-validation
Variants
Original Genome Build hg38
Number of Variants 2,321,840
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%
3 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
PPM023404 PSS012176|
African Ancestry|
7,238 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk OR: 1.49 [1.41, 1.57] AUROC: 0.612 [0.596, 0.628] — — —
PPM023414 PSS012175|
African Ancestry|
145,563 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.608 [0.601, 0.615] — — —
PPM023416 PSS012174|
African Ancestry|
3,591 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.611 [0.579, 0.642] — — —

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
PSS012174 — —
[
  • 580 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012175 — —
[
  • 6,509 cases
  • , 139,054 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — AllofUs —
PSS012176 — —
[
  • 3,478 cases
  • , 3,760 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 —