Download PGS
(Variants and weights)

Polygenic Score (PGS) ID: PGS000009

Predicted Trait

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

Score Details

Name: PRS3820_ERneg

Original Genome Build: GRCh37
Number of Variants: 3,820

PGS Development Method: LASSO penalized regression
PGS Development Details/Relevant Parameters: p < 0.001

Citation: Mavaddat N et al. Am J Hum Genet (2018) | PGS Catalog Publication ID: PGP000002

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004988
PubMed: 29059683
139,274 individuals European
Score Development/Training
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
ER-negative breast cancer cases 87,368 individuals
[ 15,404 cases, 71,964 controls]
0.0 % Male samples
ABCS, ABCFS, ABCTB, AOCS, BBCC, BCEES, BIGGS, BCINIS, BSUCH, BREOGAN, BBCS, CECILE, CTS, CPSII, CBCS, CGPS, CCGP, MISS, DIETCOMPLYF, ESTHER, GEPARSIXTO, GENICA, GESBC, GC-HBOC, HCSC, HMBCS, HUOCS, HEBCS, SZBCS, KARBAC, KBCP, ORIGO, LMBC, MMHS, MABCS, MARIE, MCBCS, MCCS, MSKCC, MBCSG, MTLGEBCS, MEC, NBHS, BCFR-NY, NBCS, NC-BCFR, OFBCR, OBCS, PREFACE, BCFR-PA, PBCS, POSH, RBCS, SBCS, SUCCESSC, SUCCESSB, SASBAC, CNIO-BCS, SKKDKFZS, SEARCH, SMC, 2SISTER, TNBCC, UCIBCS, UKOPS, PKARMA, BCFR-UTAH, WHI Training Cohort
ER-negative breast cancer cases 5,159 individuals
[ 926 cases, 4,233 controls]
0.0 % Male samples
ABCTB, BBCC, BCEES, BCINIS, BREOGAN, CTS, CPSII, CBCS, CGPS, CCGP, MISS, GENICA, HMBCS, ORIGO, LMBC, MMHS, MCBCS, MCCS, NBHS, PBCS, SEARCH, SMC, UCIBCS, PKARMA, WHI Validation Cohort

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
PPM000010 PSS000006 Mavaddat N et al. (2018) Reported Trait: ER-negative breast cancer OR: 1.44 [1.36 - 1.53] AUROC: 0.6 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
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