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(Variants and weights)

Polygenic Score (PGS) ID: PGS000003

Predicted Trait

Reported Trait: ER-negative Breast Cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): estrogen-receptor negative breast cancer

Score Details

Name: PRS77_ERneg

Original Genome Build: NR
Number of Variants: 77

PGS Development Method: SNPs passing genome-wide significance
PGS Development Details/Relevant Parameters: P<5x10-8

Citation: Mavaddat N et al. J Natl Cancer Inst (2015) | PGS Catalog Publication ID: PGP000001

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001937
PubMed: 23535729
22,627 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000003 PSS000002 Mavaddat N et al. (2015) Reported Trait: ER-negative breast cancer OR: 1.45 [1.4 - 1.49]
PPM000013 PSS000006 Mavaddat N et al. (2018) Ext. Reported Trait: ER-negative breast cancer OR: 1.35 [1.27 - 1.43] AUROC: 0.584 study, genetic PCs 1-15

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000002 ER-negative breast cancer 38,722 individuals
[ 5,738 cases, 32,984 controls]
European ABCS, ABCFS, BBCC, BIGGS, BSUCH, CECILE, CTS, CGPS, ESTHER, GENICA, HMBCS, SZBCS, pKARMA, KBCP, ORIGO, LMBC, MARIE, MCBCS, MCCS, MTLGEBCS, MEC, NBHS, NorBCS, OBCS, PBCS, RPCI, SBCS, SASBAC, SKKDKFZS, SEARCH, OSU, UKBGS, DEMOKRITOS iCOGS
PSS000006 ER-negative breast cancer cases 11,428 individuals
[ 1,259 cases, 10,169 controls]
0.0 % Male samples
European AHS, BGS, PROCAS, EPIC, FHRISK, NHS2, NHS, PLCO, KARMA, SISTER Prospective Test Set