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 categories
Cancer
Neurological disorder
Synonyms 35 synonyms
  • CNS cancer
  • CNS malignant neoplasms
  • CNS neoplasm
  • 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 cancer
  • central nervous system neoplasms, malignant
  • central nervous system tumor
  • central nervous system tumor
  • central nervous system tumors
  • central nervous system tumour
  • central nervous system tumours
  • malignant CNS neoplasm
  • malignant CNS neoplasms
  • malignant CNS tumor
  • malignant CNS tumour
  • malignant central nervous system neoplasm
  • malignant central nervous system tumor
  • malignant central nervous system tumour
  • 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
  • malignant tumour of CNS
  • malignant tumour of central nervous system
  • malignant tumour of the CNS
  • malignant tumour of the central nervous system
Mapped terms 13 mapped terms
  • DOID:3620
  • EFO:0000326
  • ICD10:C72.9
  • ICD9:239.7
  • MEDGEN:87593
  • MESH:D016543
  • MONDO:0002714
  • NANDO:2100007
  • NCIT:C4627
  • NCIT:C9293
  • OMIM:616568
  • SCTID:126951006
  • UMLS:C0348374
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 "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
GWAS
Dev
Eval
 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)
 Brain and nervous system cancer central nervous system cancer 23
https://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)
 Brain and nervous system cancer central nervous system cancer 19
https://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)
 Brain cancer 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)
 Brain cancer 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)
 Brain cancer 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)
 Brain cancer 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)
 Brain cancer 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)
 Brain cancer brain cancer 11
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000625/ScoringFiles/PGS000625.txt.gz
PGS001808
(portability-PLR_191.11)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Brain cancer brain cancer 117
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001808/ScoringFiles/PGS001808.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
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
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 —
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 —
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 —
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
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 —
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
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 —
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 —
PSS009278 — — 19,895 individuals — European UK (+ Ireland) UKB —
PSS008160 — — 6,310 individuals — South Asian India (South Asia) UKB —