Polygenic Score (PGS) ID: PGS004894

Predicted Trait
Reported Trait Estrogen receptor positive breast cancer
Mapped Trait(s) estrogen-receptor positive breast cancer (EFO_1000649)
Released in PGS Catalog: May 8, 2024
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Score Details

Score Construction
PGS Name ERpos.prs
Development Method
Name Thresholding Stepwise Forward Logistic Regression
Parameters LD r2 < 0.9, p value <0.05
Variants
Original Genome Build hg19
Number of Variants 29,309
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)		 AABC, 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
PPM021274 PSS011673|
African Ancestry|
5,821 individuals
 PGP000621 |
Gao G et al. Hum Mol Genet (2022)
 Reported Trait: Estrogen receptor positive breast cancer OR: 1.49 [1.39, 1.6] AUROC: 0.608 [0.588, 0.627] — age, consortium/study, and top 10 principal components —

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
PSS011673 — —
[
  • 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)		 — AABC, AMBER, BCAC, GBHS, ROOT —