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 Overexpressing breast carcinoma
  • HER2 Overexpressing subtype of breast carcinoma
  • HER2 Positive breast cancer
  • HER2 positive breast carcinoma
  • Her2-receptor positive breast cancer
Mapped terms 7 mapped terms
  • DOID:0060079
  • EFO:1000294
  • MEDGEN:743175
  • MONDO:0006244
  • NCIT:C53556
  • SCTID:427685000
  • UMLS:C1960398

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)
African
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Additional Asian Ancestries
European
Greater Middle Eastern
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
GWAS
Dev
Eval
 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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000215/ScoringFiles/PGS000215.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
PPM000658 PGS000215
(PRS330_HER2)
 PSS000359|
European Ancestry|
21,533 individuals
 PGP000088 |
Zhang H et al. Nat Genet (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) 		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
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