Polygenic Score (PGS) ID: PGS003380

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
PGS Name best_BRCA
Development Method
Name LDpred2
Parameters LDpred2-auto
Variants
Original Genome Build GRCh37
Number of Variants 1,142,637
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000413
Citation (link to publication) Namba S et al. Cancer Res (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
247,173 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010098
Europe PMC: 32424353
 247,173 individuals European 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
PPM016255 PSS010074|
European Ancestry|
154,361 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: breast cancer — AUROC: 0.696 R²: 0.0555 age, top 20 genetic 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
PSS010074 C50 —
[
  • 11,469 cases
  • , 142,892 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer