Trait: brain neoplasm

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003833
Description A neoplasm (disease) that involves the brain. [MONDO: patterns/location]
Trait category
Cancer
Neurological disorder
Synonyms 27 synonyms
  • Brain Neoplasms
  • Brain Tumor
  • Brain Tumor, Recurrent
  • Brain Tumors
  • Brain Tumors, Recurrent
  • INTRACRANIAL NEOPL
  • Intracranial Neoplasm
  • Intracranial Neoplasms
  • NEOPL BRAIN
  • NEOPL INTRACRANIAL
  • Neoplasm, Brain
  • Neoplasm, Intracranial
  • Neoplasms, Brain
  • Neoplasms, Intracranial
  • PRIMARY BRAIN NEOPL
  • Recurrent Brain Tumor
  • Recurrent Brain Tumors
  • Tumor, Brain
  • Tumors, Brain
  • brain neoplasm
  • brain neoplasm (disease)
  • brain neoplasms
  • brain tumor
  • neoplasm of brain
  • neoplasm of the brain
  • tumor of brain
  • tumor of the Brain
Mapped term(s) 6 mapped terms
  • COHD:373724
  • DOID:1319
  • ICD10:C71
  • MeSH:D001932
  • NCIT:C2907
  • NCIt:C2907
Child trait(s) 2 child traits

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 "brain neoplasm" 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 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
PGS000620
(PRSWEB_PHECODE191.11_C71_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 522
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000620/ScoringFiles/PGS000620.txt.gz
PGS000621
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 12
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000621/ScoringFiles/PGS000621.txt.gz
PGS000622
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_P_5e-08_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 12
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000622/ScoringFiles/PGS000622.txt.gz
PGS000623
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 11
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000623/ScoringFiles/PGS000623.txt.gz
PGS000624
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_PT_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 5
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000624/ScoringFiles/PGS000624.txt.gz
PGS000625
(PRSWEB_PHECODE191.11_UKBB-SAIGE-HRC-X191.11_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 11
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000625/ScoringFiles/PGS000625.txt.gz
PGS000781
(GRS7_Glio)
PGP000185 |
Adel Fahmideh M et al. Sci Rep (2019)
Glioma brain neoplasm,
glioma
5
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000781/ScoringFiles/PGS000781.txt.gz
PGS000781
(GRS7_Glio)
PGP000185 |
Adel Fahmideh M et al. Sci Rep (2019)
Glioma brain neoplasm,
glioma
5
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000781/ScoringFiles/PGS000781.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]
PPM001305 PGS000620
(PRSWEB_PHECODE191.11_C71_LASSOSUM_MGI_20200608)
PSS000557|
European Ancestry|
2,563 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain OR: 1.195 [1.045, 1.367]
β: 0.179 (0.0686)
AUROC: 0.546 [0.504, 0.587] Nagelkerke's Pseudo-R²: 0.00561
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 1.42 [0.453, 4.47]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.11_C71_LASSOSUM_MGI_20200608
PPM001306 PGS000621
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_P_5e-08_MGI_20200608)
PSS000557|
European Ancestry|
2,563 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain OR: 1.159 [1.015, 1.324]
β: 0.148 (0.068)
AUROC: 0.54 [0.503, 0.579] Nagelkerke's Pseudo-R²: 0.00394
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 1.02 [0.271, 3.86]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_P_5e-08_MGI_20200608
PPM001307 PGS000622
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_P_5e-08_UKB_20200608)
PSS000577|
European Ancestry|
3,020 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain OR: 1.486 [1.315, 1.679]
β: 0.396 (0.0624)
AUROC: 0.605 [0.569, 0.639] Nagelkerke's Pseudo-R²: 0.0289
Brier score: 0.0815
Odds Ratio (OR, top 1% vs. Rest): 3.38 [1.59, 7.2]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_P_5e-08_UKB_20200608
PPM001308 PGS000623
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_PT_MGI_20200608)
PSS000557|
European Ancestry|
2,563 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain OR: 1.153 [1.01, 1.316]
β: 0.142 (0.0676)
AUROC: 0.538 [0.501, 0.577] Nagelkerke's Pseudo-R²: 0.00369
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 0.602 [0.113, 3.22]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_PT_MGI_20200608
PPM001309 PGS000624
(PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_PT_UKB_20200608)
PSS000577|
European Ancestry|
3,020 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain OR: 1.515 [1.344, 1.708]
β: 0.415 (0.0611)
AUROC: 0.606 [0.568, 0.642] Nagelkerke's Pseudo-R²: 0.0326
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 4.15 [2.04, 8.41]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.11_GWAS-Catalog-r2019-05-03-X191.11_PT_UKB_20200608
PPM001310 PGS000625
(PRSWEB_PHECODE191.11_UKBB-SAIGE-HRC-X191.11_PT_MGI_20200608)
PSS000557|
European Ancestry|
2,563 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain OR: 1.142 [1.004, 1.299]
β: 0.133 (0.0657)
AUROC: 0.53 [0.492, 0.57] Nagelkerke's Pseudo-R²: 0.00328
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 2.28 [0.88, 5.88]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.11_UKBB-SAIGE-HRC-X191.11_PT_MGI_20200608
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] : 0.012 Age, sex, country

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
PSS000557 PheCode:191.11; ICD9CM:191.0, 191.1, 191.2, 191.3, 191.4, 191.5, 191.6, 191.7, 191.8, 191.9, V10.85; ICD10CM:C71, C71.0, C71.1, C71.2, C71.3, C71.4, C71.5, C71.6, C71.7, C71.8, C71.9
[
  • 233 cases
  • , 2,330 controls
]
European MGI
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
PSS000577 PheCode:191.11; ICD9:191, 191.0, 191.1, 191.2, 191.3, 191.4, 191.5, 191.6, 191.7, 191.8, 191.9; ICD10:C71.0, C71.1, C71.2, C71.3, C71.4, C71.5, C71.6, C71.7, C71.8, C71.9
[
  • 275 cases
  • , 2,745 controls
]
European UKB
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