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(Variants and weights)

Polygenic Score (PGS) ID: PGS000046

Predicted Trait

Reported Trait: Estrogen receptor [ER]-positive breast cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): estrogen-receptor positive breast cancer

Score Details

Name: BCPRS_ER+

Original Genome Build: GRCh37
Number of Variants: 87

PGS Development Method: Known susceptibility loci (genome-wide significant SNPs)
PGS Development Details/Relevant Parameters: p<5x10-8, included indpendent SNPs from fine-mapping studies (p < 10-4)

Citation: Kuchenbaecker KB et al. J Natl Cancer Inst (2017) | PGS Catalog Publication ID: PGP000033

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
PPM000108 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 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 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
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