Trait: central nervous system cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000326
Description A malignant neoplasm involving the central nervous system [MONDO: DesignPattern]
Trait category
Cancer
Neurological disorder
Synonyms 49 synonyms
  • CNS Cancer
  • CNS Malignant Neoplasms
  • CNS Neoplasms, Malignant
  • CNS cancer
  • CNS malignant neoplasms
  • CNS neoplasm
  • CNS neoplasms, malignant
  • Cancer of CNS
  • Cancer of Central Nervous System
  • Cancer of the CNS
  • Cancer of the Central Nervous System
  • Central Nervous System Neoplasms, Malignant
  • Glial Cell Tumor
  • Glioma
  • Malignant CNS Neoplasm
  • Malignant CNS Neoplasms
  • Malignant CNS Tumor
  • Malignant Central Nervous System Neoplasm
  • Malignant Central Nervous System Tumor
  • Malignant Neoplasm of CNS
  • Malignant Neoplasm of Central Nervous System
  • Malignant Neoplasm of the CNS
  • Malignant Neoplasm of the Central Nervous System
  • Malignant Tumor of CNS
  • Malignant Tumor of Central Nervous System
  • Malignant Tumor of the CNS
  • Malignant Tumor of the Central Nervous System
  • cancer of CNS
  • cancer of central nervous system
  • cancer of the CNS
  • cancer of the central nervous system
  • central nervous system cancer
  • central nervous system neoplasms, malignant
  • central nervous system tumor
  • central nervous system tumors
  • malignant CNS neoplasm
  • malignant CNS neoplasms
  • malignant CNS tumor
  • malignant central nervous system neoplasm
  • malignant central nervous system tumor
  • malignant neoplasm of CNS
  • malignant neoplasm of central nervous system
  • malignant neoplasm of the CNS
  • malignant neoplasm of the central nervous system
  • malignant tumor of CNS
  • malignant tumor of central nervous system
  • malignant tumor of the CNS
  • malignant tumor of the central nervous system
  • neoplasm of central nervous system
Mapped term(s) 15 mapped terms
  • DOID:3620
  • ICD10:C72.9
  • ICD9:239.7
  • MESH:D016543
  • MONDO:0002714
  • MeSH:D005910
  • NCIT:C4627
  • NCIt:C3059
  • NCIt:C4627
  • NIFSTD:birnlex_12618
  • OMIM:616568
  • SCTID:126951006
  • SNOMEDCT:115240006
  • SNOMEDCT:372062007
  • SNOMEDCT:393564001
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 "central nervous system cancer" 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)
PGS000618
(PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_P_5e-08_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain and nervous system central nervous system cancer 23
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000618/ScoringFiles/PGS000618.txt.gz
PGS000619
(PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_PT_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Cancer of brain and nervous system central nervous system cancer 19
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000619/ScoringFiles/PGS000619.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

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
PPM001303 PGS000618
(PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_P_5e-08_UKB_20200608)
PSS000578|
European Ancestry|
3,110 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain and nervous system OR: 1.569 [1.399, 1.759]
β: 0.45 (0.0585)
AUROC: 0.623 [0.592, 0.656] Nagelkerke's Pseudo-R²: 0.0401
Brier score: 0.0812
Odds Ratio (OR, top 1% vs. Rest): 3.64 [1.76, 7.53]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_P_5e-08_UKB_20200608
PPM001304 PGS000619
(PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_PT_UKB_20200608)
PSS000578|
European Ancestry|
3,110 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of brain and nervous system OR: 1.564 [1.396, 1.753]
β: 0.448 (0.0581)
AUROC: 0.622 [0.59, 0.653] Nagelkerke's Pseudo-R²: 0.0401
Brier score: 0.0812
Odds Ratio (OR, top 1% vs. Rest): 2.93 [1.34, 6.41]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_PT_UKB_20200608
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

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
PSS000578 PheCode:191.1; ICD9:192, 192.0, 192.1, 192.2, 192.3, 192.8, 192.9; ICD10:C70.0, C70.1, C70.9, C71.0, C71.1, C71.2, C71.3, C71.4, C71.5, C71.6, C71.7, C71.8, C71.9, C72.0, C72.1, C72.2, C72.3, C72.4, C72.5, C72.8, C72.9
[
  • 283 cases
  • , 2,827 controls
]
European 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
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