Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0005543 |
Description | A benign or malignant brain and spinal cord tumor that arises from glial cells (astrocytes, oligodendrocytes, ependymal cells). Tumors that arise from astrocytes are called astrocytic tumors or astrocytomas. Tumors that arise from oligodendrocytes are called oligodendroglial tumors. Tumors that arise from ependymal cells are called ependymomas. [NCIT: C3059] | Trait categories |
Cancer
Neurological disorder
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Synonyms |
9 synonyms
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Mapped terms |
8 mapped terms
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Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000155 (cGRS_Glioma) |
PGP000075 | Shi Z et al. Cancer Med (2019) |
Glioma | glioma | 19 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000155/ScoringFiles/PGS000155.txt.gz |
PGS000781 (GRS7_Glio) |
PGP000185 | Adel Fahmideh M et al. Sci Rep (2019) |
Glioma | brain neoplasm, glioma |
5 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000781/ScoringFiles/PGS000781.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 |
---|---|---|---|---|---|---|---|---|---|
PPM000475 | PGS000155 (cGRS_Glioma) |
PSS000275| European Ancestry| 14,419 individuals |
PGP000075 | Shi Z et al. Cancer Med (2019) |
Reported Trait: Glioma | — | — | Mean realative risk: 1.22 [1.18, 1.26] Wilcoxon test (case vs. control) p-value: 1.39e-37 |
— | — |
PPM000486 | PGS000155 (cGRS_Glioma) |
PSS000275| European Ancestry| 14,419 individuals |
PGP000075 | Shi Z et al. Cancer Med (2019) |
Reported Trait: Glioma | — | — | Odds Ratio (OR; high vs. average risk groups): 1.8 [1.55, 2.1] | — | — |
PPM002036 | PGS000781 (GRS7_Glio) |
PSS001009| Multi-ancestry (including European)| 734 individuals |
PGP000185 | Adel Fahmideh M et al. Sci Rep (2019) |
Reported Trait: Pediatric brain tumors | OR: 1.25 [1.06, 1.49] | — | R²: 0.012 | Age, sex, country | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS001009 | Cases include participants with the following tumors: Astrocytomas (ICCC-3 group IIIb), Other gliomas (ICCC-3 group IIId), Ependymomas (ICCC-3 group IIIa), Intracranial embryonal tumors (ICCC-3 group IIIc), other specified intracranial neoplasms (ICCC-3 group IIIe), unspecified intracranial neoplasms (ICCC-3 group IIIf) | — | [ ,
54.09 % Male samples |
— | European, NR | European = 454, NR =280 | CEFALO | — |
PSS000275 | Primary tumor samples from TCGA | — | [
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Mean = 52.0 years Sd = 16.0 years |
European | — | TCGA | — |
PSS000275 | — | — | [
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— | European | — | eMERGE | — |