Trait: high grade malignant neoplasm

Trait Information
Identifier MONDO_0020665
Trait category
Other trait
Synonym high grade malignant neoplasm
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 PGS for child terms of "high grade malignant neoplasm" in the EFO hierarchy.
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)
PGS000469
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Carcinoma in situ of skin skin carcinoma in situ 1,119,238
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000469/ScoringFiles/PGS000469.txt.gz
PGS000470
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Carcinoma in situ of skin skin carcinoma in situ 5
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000470/ScoringFiles/PGS000470.txt.gz
PGS000471
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Carcinoma in situ of skin skin carcinoma in situ 7
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000471/ScoringFiles/PGS000471.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
PPM001154 PGS000469
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PRS-CS_MGI_20200608)
 PSS000547|
European Ancestry|
5,500 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Carcinoma in situ of skin OR: 1.09 [1.001, 1.188]
β: 0.0865 (0.0437)		 AUROC: 0.524 [0.499, 0.549] Nagelkerke's Pseudo-R²: 0.00141
Brier score: 0.0939
Odds Ratio (OR, top 1% vs. Rest): 1.48 [0.703, 3.1]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PRS-CS_MGI_20200608
PPM001155 PGS000470
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608)
 PSS000547|
European Ancestry|
5,500 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Carcinoma in situ of skin OR: 1.308 [1.208, 1.417]
β: 0.269 (0.0407)		 AUROC: 0.557 [0.531, 0.582] Nagelkerke's Pseudo-R²: 0.0154
Brier score: 0.093
Odds Ratio (OR, top 1% vs. Rest): 2.45 [1.34, 4.45]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608
PPM001156 PGS000471
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608)
 PSS000547|
European Ancestry|
5,500 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Carcinoma in situ of skin OR: 1.401 [1.297, 1.513]
β: 0.337 (0.0393)		 AUROC: 0.569 [0.541, 0.595] Nagelkerke's Pseudo-R²: 0.0255
Brier score: 0.0923
Odds Ratio (OR, top 1% vs. Rest): 3.77 [2.24, 6.34]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608
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
PSS000547 PheCode:172.3; ICD9CM:232.0, 232.1, 232.2, 232.3, 232.4, 232.5, 232.6, 232.7, 232.8, 232.9; ICD10CM:D04, D04.0, D04.1, D04.10, D04.11, D04.12, D04.2, D04.20, D04.21, D04.22, D04.3, D04.30, D04.39, D04.4, D04.5, D04.6, D04.60, D04.61, D04.62, D04.7, D04.70, D04.71, D04.72, D04.8, D04.9 —
[
  • 585 cases
  • , 4,915 controls
]
 — European — MGI —
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