Trait: HER2 Positive Breast Carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000294
Description A biologic subset of breast carcinoma defined by high expression of HER2, GRB7, and TRAP100, and by lack of expression of estrogen receptor (ER). [NCIT: C53556]
Trait category
Cancer
Synonyms 6 synonyms
  • ERBB2 Overexpressing subtype of breast carcinoma
  • HER2 positive breast carcinoma
  • HER2 Overexpressing breast carcinoma
  • Her2-receptor positive breast cancer
  • HER2 Positive breast cancer
  • HER2 Overexpressing subtype of breast carcinoma
Mapped term(s) 6 mapped terms
  • NCIT:C53556
  • UMLS:C1960398
  • MONDO:0006244
  • NCIt:C53556
  • DOID:0060079
  • SCTID:427685000

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)
PGS000215 PRS330_HER2 PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (HER2-enriched-like) HER2 Positive Breast Carcinoma 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000215/ScoringFiles/PGS000215.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
PPM000658 PGS000215 (PRS330_HER2) PSS000359 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (HER2-enriched-like) OR: 1.53[1.42, 1.65] AUROC: 0.6208

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
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