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(Variants and weights)

Polygenic Score (PGS) ID: PGS000002

Predicted Trait

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

Score Details

Name: PRS77_ERpos

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
PPM000002 PSS000003 Mavaddat N et al. (2015) Reported Trait: ER-positive breast cancer OR: 1.63 [1.6 - 1.67]
PPM000012 PSS000005 Mavaddat N et al. (2018) Ext. Reported Trait: ER-positive breast cancer OR: 1.52 [1.48 - 1.56] AUROC: 0.615 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
PSS000003 ER-positive breast cancer 53,923 individuals
[ 21,365 cases, 32,558 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
PSS000005 ER-positive breast cancer cases 11,428 individuals
[ 7,992 cases, 3,436 controls]
0.0 % Male samples
European AHS, BGS, PROCAS, EPIC, FHRISK, NHS2, NHS, PLCO, KARMA, SISTER Prospective Test Set