Trait: estrogen-receptor negative breast cancer

Information

Experimental Factor Ontology ID: EFO_1000650

EFO Trait Description: a subtype of breast cancer that is estrogen-receptor negative [EFO: 1000650]

Associated PGS

PGS 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 Evaluated Score 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 PGS000003 (PRS77_ERneg) PSS000002 Mavaddat N et al. (2015) Reported Trait: ER-negative breast cancer OR: 1.45 [1.4 - 1.49]
PPM000013 PGS000003 (PRS77_ERneg) 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
PPM000116 PGS000003 (PRS77_ERneg) PSS000070 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.24 [1.21 - 1.28] Country, birth year
PPM000119 PGS000003 (PRS77_ERneg) PSS000071 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.13 [1.08 - 1.18] Country, birth year
PPM000007 PGS000006 (PRS313_ERneg) PSS000006 Mavaddat N et al. (2018) Reported Trait: ER-negative breast cancer OR: 1.45 [1.37 - 1.53] AUROC: 0.601 study, genetic PCs 1-15
PPM000010 PGS000009 (PRS3820_ERneg) 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
PPM000110 PGS000047 (BCPRS_ER-) PSS000070 Kuchenbaecker KB et al. (2017) Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.27 [1.23 - 1.31] C-index: 0.581 [0.571 - 0.592] Country, birth year
PPM000111 PGS000047 (BCPRS_ER-) PSS000071 Kuchenbaecker KB et al. (2017) Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.15 [1.1 - 1.2] C-index: 0.538 [0.523 - 0.553] Country, birth year
PPM000122 PGS000047 (BCPRS_ER-) PSS000074 Lecarpentier J et al. (2017) Ext. Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations OR: 1.19 [1.05 - 1.35] AUROC: 0.55 [0.51 - 0.59] 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS

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]
0.00 %% Male samples
European AHS, BGS, PROCAS, EPIC, FHRISK, NHS2, NHS, PLCO, KARMA, SISTER Prospective Test Set
PSS000070 BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. 15,252 individuals
[ 7,797 cases, 7,455 controls]
0.00 %% Male samples
European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 40
PSS000071 BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. 8,211 individuals
[ 4,330 cases, 3,881 controls]
0.00 %% Male samples
European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 43
PSS000074 Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. 1,590 individuals
[ 277 cases, 1,313 controls]
1.00 %% Male samples
European Self-reported European ancestry BFBOCC, BRICOH, BCFR, CONSIT, CBCS, Chicago, CIMBA, DKFZ, HEBON, EMBRACE, FCCC, G-FaST, GEMO, GC-HBOC, HCSC, HUNBOCS, HVH, HEBCS, ICO, IOVHBOCS, IPOBCS, MUV, MSKCC, NCI, OCGN, OUH, PBCS, CNIO, MAYO, OSU, DEMOKRITOS, ILUH, KCONFAB, SWE-BRCA, UPENN, UPITT, VFCTG