Trait: estrogen-receptor positive breast cancer

Information

Experimental Factor Ontology ID: EFO_1000649

EFO Trait Description: a subtype of breast cancer that is estrogen-receptor positive [EFO: 1000649]

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
PPM000002 PGS000002 (PRS77_ERpos) PSS000003 Mavaddat N et al. (2015) Reported Trait: ER-positive breast cancer OR: 1.63 [1.6 - 1.67]
PPM000012 PGS000002 (PRS77_ERpos) 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
PPM000115 PGS000002 (PRS77_ERpos) PSS000070 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.09 [1.06 - 1.12] Country, birth year
PPM000118 PGS000002 (PRS77_ERpos) PSS000071 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.17 - 1.27] Country, birth year
PPM000006 PGS000005 (PRS313_ERpos) PSS000005 Mavaddat N et al. (2018) Reported Trait: ER-positive breast cancer OR: 1.68 [1.63 - 1.73] AUROC: 0.641 study, genetic PCs 1-15
PPM000009 PGS000008 (PRS3820_ERpos) PSS000005 Mavaddat N et al. (2018) Reported Trait: ER-positive breast cancer OR: 1.73 [1.68 - 1.78] AUROC: 0.647 study, genetic PCs 1-15
PPM000108 PGS000046 (BCPRS_ER+) PSS000070 Kuchenbaecker KB et al. (2017) Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.11 [1.08 - 1.15] C-index: 0.532 [0.522 - 0.543] Country, birth year
PPM000109 PGS000046 (BCPRS_ER+) PSS000071 Kuchenbaecker KB et al. (2017) Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.16 - 1.27] C-index: 0.566 [0.551 - 0.581] Country, birth year
PPM000121 PGS000046 (BCPRS_ER+) PSS000074 Lecarpentier J et al. (2017) Ext. Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations OR: 1.36 [1.19 - 1.56] AUROC: 0.59 [0.55 - 0.63] 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
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]
0.00 %% 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