Trait: triple-negative breast cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005537
Description An invasive breast carcinoma which is negative for expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). [NCIT: P378]
Trait category
Synonyms 4 synonyms
  • TNBC
  • triple-negative breast cancer
  • triple-negative breast carcinoma
  • triple-receptor negative breast cancer
Mapped terms 8 mapped terms
  • DOID:0060081
  • EFO:0005537
  • MESH:D064726
  • MONDO:0005494
  • NCIT:C71732
  • SCTID:706970001
  • UMLS:C3539878
  • UMLS:C4722518

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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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
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Additional Asian Ancestries
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
Scoring File (FTP Link)
PGP000088 |
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (triple negative) triple-negative breast cancer 330

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000661 PGS000216
European Ancestry|
22,821 individuals
PGP000088 |
Zhang H et al. Nat Genet (2020)
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.65 [1.57, 1.73] AUROC: 0.6358

Evaluated Samples

PGS Sample Set 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
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
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data