Trait: brain neoplasm

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003833
Description A neoplasm (disease) that involves the brain. [MONDO: patterns/location]
Trait categories
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 terms 6 mapped terms
  • DOID:1319
  • ICD10:C71
  • MeSH:D001932
  • MedDRA:10061019
  • NCIT:C2907
  • NCIt:C2907
Child trait(s) brain cancer

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 Scoring File (FTP Link)
PGS000620
(PRSWEB_PHECODE191.11_C71_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain brain cancer 522
https://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
https://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
https://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
https://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
https://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
https://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
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000781/ScoringFiles/PGS000781.txt.gz
PGS001808
(portability-PLR_191.11)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Cancer of brain brain cancer 117
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001808/ScoringFiles/PGS001808.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
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
PPM009367 PGS001808
(portability-PLR_191.11)
PSS009278|
European Ancestry|
19,895 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0144 sex, age, birth date, deprivation index, 16 PCs
PPM009368 PGS001808
(portability-PLR_191.11)
PSS009052|
European Ancestry|
4,114 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0179 [-0.0128, 0.0485] sex, age, birth date, deprivation index, 16 PCs
PPM009369 PGS001808
(portability-PLR_191.11)
PSS008606|
European Ancestry|
6,626 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0237 sex, age, birth date, deprivation index, 16 PCs
PPM009370 PGS001808
(portability-PLR_191.11)
PSS008160|
South Asian Ancestry|
6,310 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0098 [-0.0149, 0.0345] sex, age, birth date, deprivation index, 16 PCs
PPM009371 PGS001808
(portability-PLR_191.11)
PSS007947|
East Asian Ancestry|
1,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0004 [-0.0461, 0.0468] sex, age, birth date, deprivation index, 16 PCs
PPM009372 PGS001808
(portability-PLR_191.11)
PSS007729|
African Ancestry|
2,477 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0217 [-0.0179, 0.0612] sex, age, birth date, deprivation index, 16 PCs
PPM009373 PGS001808
(portability-PLR_191.11)
PSS008832|
African Ancestry|
3,913 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0343 [0.0029, 0.0657] sex, age, birth date, deprivation index, 16 PCs

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
PSS008832 3,913 individuals African unspecified Nigeria (West Africa) UKB
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
PSS007947 1,801 individuals East Asian China (East Asia) UKB
PSS007729 2,477 individuals African American or Afro-Caribbean Carribean UKB
PSS008606 6,626 individuals European Italy (South Europe) UKB
PSS009052 4,114 individuals European Poland (NE Europe) UKB
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
PSS009278 19,895 individuals European UK (+ Ireland) UKB
PSS008160 6,310 individuals South Asian India (South Asia) UKB