Trait: breast tumor luminal

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000306
Description A biologic subset of breast carcinoma defined by low to moderate expression of genes characteristic of luminal epithelial cells including estrogen receptor (ER), and high expression of GGH, LAPTM4B, and CCNE1. This subtype of breast cancer is associated with a good prognosis, although not as favorable as the luminal A subtype. [NCIT: P378]
Trait category
Cancer
Synonyms 5 synonyms
  • luminal breast cancer
  • breast tumor luminal A or B
  • Luminal B Breast Carcinoma
  • Luminal A Breast Carcinoma
  • breast tumor luminal
Mapped term(s) 4 mapped terms
  • DOID:0060548
  • MONDO:0004990
  • NCIt:C53554
  • NCIt:C53555

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)
PGS000212 PRS330_LumA PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (luminal A-like) breast tumor luminal 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000212/ScoringFiles/PGS000212.txt.gz
PGS000214 PRS330_LumB PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (luminal B-like) breast tumor luminal 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000214/ScoringFiles/PGS000214.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
PPM000649 PGS000212 (PRS330_LumA) PSS000360 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (luminal A-like) OR: 1.83[1.78, 1.88] AUROC: 0.6609
PPM000655 PGS000214 (PRS330_LumB) PSS000362 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (luminal B-like) OR: 1.69[1.61, 1.77] AUROC: 0.6431

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
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
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