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(Variants and weights)

Polygenic Score (PGS) ID: PGS000004

Predicted Trait

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

Score Details

Name: PRS313_BC

Original Genome Build: GRCh37
Number of Variants: 313

PGS Development Method: Hard-Thresholding Stepwise Forward Regression
PGS Development Details/Relevant Parameters: p < 10^-5

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
Invasive breast cancer-affected 158,648 individuals
[ 88,916 cases, 69,732 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
Invasive breast cancer-affected 10,444 individuals
[ 5,159 cases, 5,285 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
PPM000004 PSS000004 Mavaddat N et al. (2018) Reported Trait: Invasive breast cancer OR: 1.61 [1.57 - 1.65] AUROC: 0.63 study, genetic PCs 1-15
PPM000005 PSS000007 Mavaddat N et al. (2018) Reported Trait: Incident breast cancer cases HR: 1.59 [1.54 - 1.64] study, genetic PCs 1-15 Included only 306 of the 313 SNPs

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
PSS000004 Invasive breast cancer-affected 29,751 individuals
[ 11,428 cases, 18,323 controls]
0.0 % Male samples
European AHS, BGS, PROCAS, EPIC, FHRISK, NHS2, NHS, PLCO, KARMA, SISTER Prospective Test Set
PSS000007 Incident registry-confirmed invasive breast cancers developed 190,040 individuals
[ 3,215 cases, 186,825 controls]
0.0 % Male samples
European UKB Prospective Test Set (UKB)