Polygenic Score (PGS) ID: PGS000003

Predicted Trait
Reported Trait ER-negative Breast Cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name PRS77_ERneg
Variants
Original Genome Build NR
Number of Variants 77
Development Method
Name SNPs passing genome-wide significance
Parameters P<5x10-8
PGS Source
PGS Catalog Publication (PGP) ID PGP000001
Citation (link to publication) Mavaddat N et al. J Natl Cancer Inst (2015)

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
PPM000119 PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.13[1.08, 1.18] Country, birth year
PPM000116 PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.24[1.21, 1.28] Country, birth year
PPM000003 PSS000002 PGP000001
Mavaddat N et al. (2015)
Reported Trait: ER-negative breast cancer OR: 1.45[1.4, 1.49]
PPM000013 PSS000006 PGP000002
Mavaddat N et al. (2018)
Ext.
Reported Trait: ER-negative breast cancer OR: 1.35[1.27, 1.43] AUROC: 0.584 study, genetic PCs 1-15

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
PSS000006 ER-negative breast cancer cases
[
  • 1,259 cases
  • , 10,169 controls
]
,
0.0 % Male samples
European 10 cohorts
  • AHS
  • ,BGS
  • ,EPIC
  • ,FHRISK
  • ,KARMA
  • ,NHS
  • ,NHS2
  • ,PLCO
  • ,PROCAS
  • ,SISTER
Prospective Test Set
PSS000002 ER-negative breast cancer
[
  • 5,738 cases
  • , 32,984 controls
]
European 33 cohorts
  • ABCFS
  • ,ABCS
  • ,BBCC
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HMBCS
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBHS
  • ,NorBCS
  • ,OBCS
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,pKARMA
iCOGS
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