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 |
6 mapped terms
|
Child trait(s) | triple-negative breast cancer |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | 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 |
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 | — | — | — |
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-). | — | [ ,
0.0 % Male samples |
— | European | — | 6 cohorts
|
Heldout subset (20%) of the BCAC consortium data |
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) | — | [ ,
0.0 % Male samples |
— | European | — | 6 cohorts
|
Heldout subset (20%) of the BCAC consortium data |