Trait: HER2 negative breast carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009780
Description A biologic subset of breast carcinoma defined by absence of HER2.
Trait category
Cancer
Synonym Her2-receptor negative breast cancer
Mapped terms 7 mapped terms
  • DOID:0060080
  • MEDGEN:1684659
  • MONDO:0000618
  • NCIT:C168519
  • SCTID:431396003
  • UMLS:C4733095
  • https://www.cancer.gov/publications/dictionaries/cancer-terms/def/her2-negative
Child trait(s) triple-negative breast cancer

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:
Display options:
Ancestry legend
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 all PGS for "HER2 negative breast carcinoma" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS000213
(PRS330_LumBHER2neg)
 PGP000088 |
Zhang H et al. Nat Genet (2020)
 Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) HER2 negative breast carcinoma 330
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000213/ScoringFiles/PGS000213.txt.gz
PGS000216
(PRS330_TN)
 PGP000088 |
Zhang H et al. Nat Genet (2020)
 Breast cancer intrinsic-like subtype (triple negative) triple-negative breast cancer 330
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000216/ScoringFiles/PGS000216.txt.gz
PGS004890
(CC-GWAS_PRS)
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Triple negative breast cancer versus luminal breast cancer triple-negative breast cancer 25
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004890/ScoringFiles/PGS004890.txt.gz
PGS004891
(TNBC_PRS25)
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Triple negative breast cancer triple-negative breast cancer 25
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004891/ScoringFiles/PGS004891.txt.gz
PGS004892
(TNBC_PRS41)
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Triple negative breast cancer triple-negative breast cancer 41
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004892/ScoringFiles/PGS004892.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
PPM000652 PGS000213
(PRS330_LumBHER2neg)
 PSS000361|
European Ancestry|
22,594 individuals
 PGP000088 |
Zhang H et al. Nat Genet (2020)
 Reported Trait: Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) OR: 1.62 [1.54, 1.7] AUROC: 0.633 — — —
PPM000661 PGS000216
(PRS330_TN)
 PSS000363|
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 — — —
PPM021270 PGS004890
(CC-GWAS_PRS)
 PSS011672|
Multi-ancestry (including European)|
9,868 individuals
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Reported Trait: Triple negative breast cancer compared to luminal-like breast cancer — — Odds ratio (OR, high vs low tertile): 2.62 [1.44, 4.75] Age at initial pathologic diagnosis of breast cancer, pathologic stage —
PPM021271 PGS004891
(TNBC_PRS25)
 PSS011672|
Multi-ancestry (including European)|
9,868 individuals
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Reported Trait: Triple negative breast cancer — — Odds ratio (OR, high vs low tertile): 1.54 [0.92, 2.59] Age at initial pathologic diagnosis of breast cancer, pathologic stage —
PPM021272 PGS004892
(TNBC_PRS41)
 PSS011672|
Multi-ancestry (including European)|
9,868 individuals
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Reported Trait: Triple negative breast cancer — — Odds ratio (OR, high vs low tertile): 1.53 [0.92, 2.55] Age at initial pathologic diagnosis of breast cancer, pathologic stage —

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
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
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
 Heldout subset (20%) of the BCAC consortium data
PSS011672 The molecular intrinsic subtypes of breast cancer were determined following the strategy of Giovanni's work using the PAM50 classifier in the TCGA-BRCA. Basal-like and luminal-like breast cancer were determined by PAM50. —
[
  • 108 cases
  • , 565 controls
]
 — European — TCGA —
PSS011672 Triple-negative breast cancer (TNBC) was defined as ER negative, PR negative and HER2 negative. The luminal breast cancer was defined as ER and/or PR positive. —
[
  • 2,321 cases
  • , 6,874 controls
]
 — African American or Afro-Caribbean — AABCG —
PSS000361 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (2) luminal B/HER2-negative-like (ER+ and/or PR+, HER2-, grade 3) —
[
  • 1,779 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