Trait: breast tumor luminal

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000306
Description Subsets of breast carcinoma defined by expression of genes characteristic of luminal epithelial cells. [NCIT: C53554] [NCIT: C53555]
Trait category
Cancer
Synonyms 5 synonyms
  • breast tumor luminal
  • breast tumor luminal A or B
  • breast tumour luminal
  • luminal breast cancer
  • luminal breast carcinoma
Mapped terms 3 mapped terms
  • DOID:0060548
  • EFO:0000306
  • MONDO:0004990
Child trait(s) 2 child traits

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows PGS for child terms of "breast tumor luminal" in the EFO hierarchy.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000212
(PRS330_LumA)
 PGP000088 |
Zhang H et al. Nat Genet (2020)
 Breast cancer intrinsic-like subtype (luminal A-like) luminal A breast carcinoma 330
-
 https://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) luminal B breast carcinoma 330
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000214/ScoringFiles/PGS000214.txt.gz

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) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000649 PGS000212
(PRS330_LumA)
 PSS000360|
European Ancestry|
28,140 individuals
 PGP000088 |
Zhang H et al. Nat Genet (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|
European Ancestry|
22,497 individuals
 PGP000088 |
Zhang H et al. Nat Genet (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) 		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
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