Trait: estrogen-receptor negative breast cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000650
Description A subtype of breast cancer that is estrogen-receptor negative [EFO: 1000650]
Trait category
Cancer
Synonyms 2 synonyms
  • estrogen-receptor negative breast cancer
  • ER- breast cancer
Mapped term(s) 3 mapped terms
  • MONDO:0006513
  • DOID:0060076
  • DOID:0060078
Child trait(s) triple-negative breast cancer

Associated Polygenic Score(s)

Note: This table shows all PGS for "estrogen-receptor negative breast cancer" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000003 PRS77_ERneg PGP000001 Mavaddat N et al. J Natl Cancer Inst (2015) ER-negative Breast Cancer estrogen-receptor negative breast cancer 77 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000003/ScoringFiles/PGS000003.txt.gz
PGS000006 PRS313_ERneg PGP000002 Mavaddat N et al. Am J Hum Genet (2018) ER-negative Breast Cancer estrogen-receptor negative breast cancer 313 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000006/ScoringFiles/PGS000006.txt.gz
PGS000009 PRS3820_ERneg PGP000002 Mavaddat N et al. Am J Hum Genet (2018) ER-negative Breast Cancer estrogen-receptor negative breast cancer 3,820 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000009/ScoringFiles/PGS000009.txt.gz
PGS000047 BCPRS_ER- PGP000033 Kuchenbaecker KB et al. J Natl Cancer Inst (2017) Estrogen receptor [ER]-negative breast cancer estrogen-receptor negative breast cancer 53 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000047/ScoringFiles/PGS000047.txt.gz
PGS000216 PRS330_TN PGP000088 Zhang H et al. Nat Genet (2020) Breast cancer intrinsic-like subtype (triple negative) triple-negative breast cancer 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000216/ScoringFiles/PGS000216.txt.gz

PGS 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)
Evaluated Score 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
PPM000007 PGS000006 (PRS313_ERneg) PSS000006 PGP000002
Mavaddat N et al. (2018)
Reported Trait: ER-negative breast cancer OR: 1.45[1.37, 1.53] AUROC: 0.601 study, genetic PCs 1-15
PPM000010 PGS000009 (PRS3820_ERneg) PSS000006 PGP000002
Mavaddat N et al. (2018)
Reported Trait: ER-negative breast cancer OR: 1.44[1.36, 1.53] AUROC: 0.6 study, genetic PCs 1-15
PPM000013 PGS000003 (PRS77_ERneg) 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
PPM000122 PGS000047 (BCPRS_ER-) 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
PPM000661 PGS000216 (PRS330_TN) PSS000363 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.65[1.57, 1.73] AUROC: 0.6358
PPM000110 PGS000047 (BCPRS_ER-) 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
PPM000111 PGS000047 (BCPRS_ER-) 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
PPM000116 PGS000003 (PRS77_ERneg) 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
PPM000119 PGS000003 (PRS77_ERneg) 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
PPM000003 PGS000003 (PRS77_ERneg) PSS000002 PGP000001
Mavaddat N et al. (2015)
Reported Trait: ER-negative breast cancer OR: 1.45[1.4, 1.49]
PPM000950 PGS000006 (PRS313_ERneg) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.24[1.16, 1.33] Country
PPM000949 PGS000006 (PRS313_ERneg) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.25[1.17, 1.33] Country
PPM000967 PGS000006 (PRS313_ERneg) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.24[1.16, 1.33] Country
PPM000966 PGS000006 (PRS313_ERneg) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.25[1.17, 1.33] Country

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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
PSS000484 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 1,027 cases
  • , 55,041 controls
]
,
0.0 % Male samples
Median (Age At Diagnosis) = 56.0 years European 41 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,KCONFAB/AOCSS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS
PSS000486 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 923 cases
  • , 55,145 controls
]
,
0.0 % Male samples
Median (Age At Diagnosis) = 56.0 years European 41 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,KCONFAB/AOCSS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS
PSS000363 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (5) triple-negative ( ER-, PR-, HER2-). 
[
  • 2,006 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data
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
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
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
]
,
100.0 % 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