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 categories
Cancer
Neurological disorder
Synonyms 9 synonyms
  • glial neoplasm
  • glial tumor
  • glioma
  • neoplasm of neuroglia
  • neoplasm of the neuroglia
  • neuroglial neoplasm
  • neuroglial tumor
  • tumor of neuroglia
  • tumor of the neuroglia
Mapped terms 9 mapped terms
  • GARD:0006513
  • MESH:D005910
  • MONDO:0021042
  • NCIT:C3059
  • OMIM:613028
  • OMIM:613029
  • Orphanet:182067
  • SCTID:393564001
  • UMLS:C0017638
Child trait(s) glioblastoma

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 "glioma" 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 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
PGS002302
(PRS28_glioma)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Glioma glioma 28
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002302/ScoringFiles/PGS002302.txt.gz
PGS003384
(best_GBM)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Glioblastoma glioblastoma 910
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003384/ScoringFiles/PGS003384.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
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 —
PPM013031 PGS002302
(PRS28_glioma)
 PSS009663|
European Ancestry|
312 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Glioma — AUROC: 0.61 [0.57, 0.64] — — —
PPM013039 PGS002302
(PRS28_glioma)
 PSS009663|
European Ancestry|
312 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Glioma — — Hazard ratio (HR top 5% vs average): 2.55 [1.72, 3.77] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM016259 PGS003384
(best_GBM)
 PSS010078|
European Ancestry|
269,806 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: glioblastoma — AUROC: 0.758 R²: 0.0216 age, sex, top 20 genetic principal components —

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
PSS009663 glioma (ICD-9 = 191 or ICD-10 = C71; ICD-O: 9380-9480) — 312 individuals — European — UKB —
PSS010078 C71, histology was either Giant cell glioblastoma or Glioblastoma (NOS) —
[
  • 262 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer
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 —
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) —
[
  • 245 cases
  • , 489 controls
]
,
54.09 % Male samples
 — European, NR European = 454, NR =280 CEFALO —