Polygenic Score (PGS) ID: PGS000155

Predicted Trait
Reported Trait Glioma
Mapped Trait(s) glioma (EFO_0005543)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Glioma
Variants
Original Genome Build NR
Number of Variants 19
Development Method
Name Pruning + Thresholding
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004347
EuropePMC: 28346443
30,659 individuals European
GWAS Catalog: GCST004348
EuropePMC: 28346443
24,009 individuals European
GWAS Catalog: GCST004349
EuropePMC: 28346443
24,381 individuals European
GWAS Catalog: GCST000439
EuropePMC: 19578367
5,548 individuals European
GWAS Catalog: GCST003227
EuropePMC: 26424050
9,799 individuals European
GWAS Catalog: GCST003220
EuropePMC: 26424050
9,218 individuals European

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 ID)
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
PPM000486 PSS000275 PGP000075
Shi Z et al. (2019)
Reported Trait: Glioma Odds Ratio (OR; high vs. average risk groups): 1.8[1.55, 2.1]
PPM000475 PSS000275 PGP000075
Shi Z et al. (2019)
Reported Trait: Glioma Mean realative risk: 1.22[1.18, 1.26]
Wilcoxon test (case vs. control) p-value: 1.39e-37

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000275 Primary tumor samples from TCGA
[
  • 992 cases
  • , 0 controls
]
Mean = 52.0 years
Sd = 16.0 years
European TCGA
PSS000275
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE