Trait Information | |
Identifier | MONDO_0001657 |
Description | A primary or metastatic malignant neoplasm affecting the brain. [NCIT: C3568] | Trait category |
Cancer
Neurological disorder
|
Synonyms |
13 synonyms
|
Mapped term(s) |
12 mapped terms
|
Polygenic Score (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS 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 | 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 |
PGS Performance Metric ID (PPM ID) |
Evaluated Score |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|---|
PPM001305 | PGS000620 (PRSWEB_PHECODE191.11_C71_LASSOSUM_MGI_20200608) | PSS000557 | PGP000118 Fritsche LG et al. (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 | PGP000118 Fritsche LG et al. (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 | PGP000118 Fritsche LG et al. (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 | PGP000118 Fritsche LG et al. (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 | PGP000118 Fritsche LG et al. (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 | PGP000118 Fritsche LG et al. (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 |
PGS Sample Set ID (PSS ID) |
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 | — | [
|
— | 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 | — | [
|
— | European | — | UKB | — |