Polygenic Score (PGS) ID: PGS000047

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Predicted Trait
Reported Trait Estrogen receptor [ER]-negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS: Dec. 18, 2019

Score Details

Score Construction
PGS Name BCPRS_ER-
Variants
Original Genome Build GRCh37
Number of Variants 53
Development Method
Name Known susceptibility loci (genome-wide significant SNPs)
Parameters p<5x10-8, included indpendent SNPs from fine-mapping studies (p < 10-4)
PGS Source
PGS Catalog Publication (PGP) ID PGP000033
Citation (link to publication) Kuchenbaecker KB et al. J Natl Cancer Inst (2017)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001937
EuropePMC: 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 ID
(PPM ID) 		PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000111 PSS000071 PGP000033
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 —
PPM000110 PSS000070 PGP000033
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 —
PPM000122 PSS000074 PGP000034
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 Sample Set ID
(PSS ID) 		Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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. —
[
  • 277 cases
  • , 1,313 controls
]
,
1.0 % Male samples
 — European Self-reported European ancestry 37 cohorts
  • BCFR
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CIMBA
  • ,CNIO
  • ,CONSIT
  • ,Chicago
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,KCONFAB
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSU
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
 —
PSS000070 BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. —
[
  • 7,797 cases
  • , 7,455 controls
]
,
0.0 % 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. —
[
  • 4,330 cases
  • , 3,881 controls
]
,
0.0 % Male samples
 — European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 43