Polygenic Score (PGS) ID: PGS000152

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) bladder carcinoma (EFO_0000292)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Bladder
Variants
Original Genome Build NR
Number of Variants 10
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: GCST002240
EuropePMC: 24163127
6,206 individuals European
GWAS Catalog: GCST000454
EuropePMC: 1964892
1,926 individuals European
GWAS Catalog: GCST001153
EuropePMC: 21750109
43,837 individuals European
(Netherlands)
GWAS Catalog: GCST002460
EuropePMC: 24861552
91,850 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
PPM000483 PSS000272 PGP000075
Shi Z et al. (2019)
Reported Trait: Bladder cancer Odds Ratio (OR; high vs. average risk groups): 1.58[1.1, 2.25]
PPM000472 PSS000272 PGP000075
Shi Z et al. (2019)
Reported Trait: Bladder cancer Mean realative risk: 1.04[1.0, 1.08]
Wilcoxon test (case vs. control) p-value: 0.00377

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
PSS000272
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
PSS000272 Primary tumor samples from TCGA
[
  • 343 cases
  • , 0 controls
]
Mean = 69.0 years
Sd = 10.0 years
European TCGA