Polygenic Score (PGS) ID: PGS000152

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) bladder carcinoma (EFO_0000292)
Released in PGS Catalog: April 29, 2020
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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)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
143,819 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002240
Europe PMC: 24163127
6,206 individuals European
GWAS Catalog: GCST000454
Europe PMC: 1964892
1,926 individuals European
GWAS Catalog: GCST001153
Europe PMC: 21750109
43,837 individuals European
(Netherlands)
GWAS Catalog: GCST002460
Europe PMC: 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)
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
PPM000472 PSS000272|
European Ancestry|
13,770 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Bladder cancer Mean realative risk: 1.04 [1.0, 1.08]
Wilcoxon test (case vs. control) p-value: 0.00377
PPM000483 PSS000272|
European Ancestry|
13,770 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Bladder cancer Odds Ratio (OR; high vs. average risk groups): 1.58 [1.1, 2.25]

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
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