Trait: glioma

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 category
Cancer
Neurological disorder
Synonyms 16 synonyms
  • GLIOMA, MALIGNANT
  • Malignant Glial Neoplasm
  • Malignant Glial Tumor
  • Malignant Glioma
  • Malignant Neuroglial Neoplasm
  • Malignant Neuroglial Tumor
  • brain glioma
  • glial neoplasm
  • glial tumor
  • glioma
  • neoplasm of neuroglia
  • neoplasm of the neuroglia
  • neuroglial neoplasm
  • neuroglial tumor
  • tumor of neuroglia
  • tumor of the neuroglia
Mapped term(s) 9 mapped terms
  • DOID:0060108
  • GARD:0006513
  • MESH:D005910
  • NCIT:C3059
  • NCIt:C4822
  • OMIM:613028
  • OMIM:613029
  • SCTID:393564001
  • UMLS:C0017638

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)
PGS000155 cGRS_Glioma PGP000075 Shi Z et al. Cancer Med (2019) Glioma glioma 19 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000155/ScoringFiles/PGS000155.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
PPM000475 PGS000155 (cGRS_Glioma) PSS000275 PGP000075 Shi Z et al. (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 PGP000075 Shi Z et al. (2019) Reported Trait: Glioma — — Odds Ratio (OR; high vs. average risk groups): 1.8 [1.55, 2.1] — —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000275 Primary tumor samples from TCGA —
[
  • 992 cases
  • , 0 controls
]
 Mean = 52.0 years
Sd = 16.0 years		 European — TCGA —
PSS000275 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —