Trait: estrogen-receptor positive breast cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000649
Description A subtype of breast cancer that is estrogen-receptor positive [EFO: 1000649]
Trait category
Cancer
Synonyms 3 synonyms
  • ER+ breast cancer
  • estrogen receptor positive breast cancer
  • estrogen-receptor positive breast cancer
Mapped term(s) 2 mapped terms
  • MONDO:0006512
  • DOID:0060075

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000002 PRS77_ERpos PGP000001
Mavaddat N et al. J Natl Cancer Inst (2015)
ER-positive Breast Cancer estrogen-receptor positive breast cancer 77 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000002/ScoringFiles/PGS000002.txt.gz
PGS000005 PRS313_ERpos PGP000002
Mavaddat N et al. Am J Hum Genet (2018)
ER-positive Breast Cancer estrogen-receptor positive breast cancer 313 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000005/ScoringFiles/PGS000005.txt.gz
PGS000008 PRS3820_ERpos PGP000002
Mavaddat N et al. Am J Hum Genet (2018)
ER-positive Breast Cancer estrogen-receptor positive breast cancer 3,820 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000008/ScoringFiles/PGS000008.txt.gz
PGS000046 BCPRS_ER+ PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Estrogen receptor [ER]-positive breast cancer estrogen-receptor positive breast cancer 87 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000046/ScoringFiles/PGS000046.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
PPM000006 PGS000005 (PRS313_ERpos) PSS000005 PGP000002
Mavaddat N et al. (2018)
Reported Trait: ER-positive breast cancer OR: 1.68[1.63, 1.73] AUROC: 0.641 study, genetic PCs 1-15
PPM000009 PGS000008 (PRS3820_ERpos) PSS000005 PGP000002
Mavaddat N et al. (2018)
Reported Trait: ER-positive breast cancer OR: 1.73[1.68, 1.78] AUROC: 0.647 study, genetic PCs 1-15
PPM000012 PGS000002 (PRS77_ERpos) PSS000005 PGP000002
Mavaddat N et al. (2018)
Ext.
Reported Trait: ER-positive breast cancer OR: 1.52[1.48, 1.56] AUROC: 0.615 study, genetic PCs 1-15
PPM000121 PGS000046 (BCPRS_ER+) PSS000074 PGP000034
Lecarpentier J et al. (2017)
Ext.
Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations OR: 1.36[1.19, 1.56] AUROC: 0.59[0.55, 0.63] 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
PPM000108 PGS000046 (BCPRS_ER+) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.11[1.08, 1.15] C-index: 0.532[0.522, 0.543] Country, birth year
PPM000109 PGS000046 (BCPRS_ER+) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22[1.16, 1.27] C-index: 0.566[0.551, 0.581] Country, birth year
PPM000663 PGS000005 (PRS313_ERpos) PSS000363 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.59[1.51, 1.66] AUROC: 0.6276
PPM000660 PGS000005 (PRS313_ERpos) PSS000359 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (HER2-enriched-like) OR: 1.59[1.48, 1.71] AUROC: 0.6291
PPM000657 PGS000005 (PRS313_ERpos) PSS000362 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal B-like) OR: 1.66[1.58, 1.75] AUROC: 0.64
PPM000654 PGS000005 (PRS313_ERpos) PSS000361 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) OR: 1.62[1.54, 1.7] AUROC: 0.6323
PPM000651 PGS000005 (PRS313_ERpos) PSS000360 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal A-like) OR: 1.82[1.77, 1.87] AUROC: 0.6595
PPM000115 PGS000002 (PRS77_ERpos) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.09[1.06, 1.12] Country, birth year
PPM000118 PGS000002 (PRS77_ERpos) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22[1.17, 1.27] Country, birth year
PPM000002 PGS000002 (PRS77_ERpos) PSS000003 PGP000001
Mavaddat N et al. (2015)
Reported Trait: ER-positive breast cancer OR: 1.63[1.6, 1.67]

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
PSS000003 ER-positive breast cancer
[
  • 21,365 cases
  • , 32,558 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
PSS000359 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (4) HER2-enriched-like (ER- and PR-, HER2+)
[
  • 718 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
PSS000360 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (1) luminal A-like (ER+ and/or PR+, HER2-, grade 1 & 2); 
[
  • 7,325 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
PSS000361 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (2) luminal B/HER2-negative-like (ER+ and/or PR+, HER2-, grade 3)
[
  • 1,779 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
PSS000362 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (3) luminal B-like (ER+ and/or PR+, HER2+); 
[
  • 1,682 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
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
PSS000005 ER-positive breast cancer cases
[
  • 7,992 cases
  • , 3,436 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