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(Variants and weights)

Polygenic Score (PGS) ID: PGS000001

Predicted Trait

Reported Trait: Breast Cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): breast carcinoma

Score Details

Name: PRS77_BC

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
PPM000001 PSS000001 Mavaddat N et al. (2015) Reported Trait: All breast cancer OR: 1.55 [1.52 - 1.58] C-index: 0.622 [0.619 - 0.627]
PPM000011 PSS000004 Mavaddat N et al. (2018) Ext. Reported Trait: Invasive breast cancer OR: 1.46 [1.42 - 1.49] AUROC: 0.603 study, genetic PCs 1-15
PPM000114 PSS000070 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.13 [1.1 - 1.16] Country, birth year
PPM000117 PSS000071 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.17 - 1.28] Country, birth year

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
PSS000001 All breast cancer 67,054 individuals
[ 33,673 cases, 33,381 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
PSS000004 Invasive breast cancer-affected 29,751 individuals
[ 11,428 cases, 18,323 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