Polygenic Score (PGS) ID: PGS000152

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) urinary bladder carcinoma (MONDO_0004986)
Released in PGS Catalog: April 29, 2020
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Score Details

Score Construction
PGS Name cGRS_Bladder
Development Method
Name Pruning and Thresholding (P+T)
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.
Variants
Original Genome Build NR
Number of Variants 10
Effect Weight Type Odds Ratio over expected risk
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 Cohort(s)
GWAS Catalog: GCST002240
Europe PMC: 24163127
 6,206 individuals European NR
GWAS Catalog: GCST000454
Europe PMC: 1964892
 1,926 individuals European NR
GWAS Catalog: GCST001153
Europe PMC: 21750109
 43,837 individuals European
(Netherlands)		 ICR, NBCS, NBS, UMC, deCODE
GWAS Catalog: GCST002460
Europe PMC: 24861552
 91,850 individuals European ICR, deCODE

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 —