Polygenic Score (PGS) ID: PGS000612

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) urinary bladder carcinoma (MONDO_0004986)
Additional Trait Information PheCode 189.2
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE189.2_GWAS-Catalog-r2019-05-03-X189.2_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
Variants
Original Genome Build GRCh37
Number of Variants 13
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
248,538 individuals (100%)
Score Development/Training
European: 100%
7,469 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: GCST000231
Europe PMC: 18794855
 36,139 individuals European NR
GWAS Catalog: GCST000454
Europe PMC: 19648920
 1,926 individuals European NR
GWAS Catalog: GCST000639
Europe PMC: 20348956
 41,199 individuals European NR
GWAS Catalog: GCST000842
Europe PMC: 20972438
 8,652 individuals European NR
GWAS Catalog: GCST001153
Europe PMC: 21750109
 43,837 individuals European
(Netherlands)		 NR
GWAS Catalog: GCST002240
Europe PMC: 24163127
 6,206 individuals European NR
GWAS Catalog: GCST002243
Europe PMC: 24163127
 18,729 individuals European NR
GWAS Catalog: GCST002460
Europe PMC: 24861552
 91,850 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 786 cases
  • , 6,683 controls
]
 European MGI PheCode:189.2; ICD9CM:188.0, 188.1, 188.2, 188.3, 188.4, 188.5, 188.6, 188.7, 188.8, 188.9, 233.7, 236.7, 239.4, V10.51; ICD10CM:C67, C67.0, C67.1, C67.2, C67.3, C67.4, C67.5, C67.6, C67.7, C67.8, C67.9, D09.0, D41.4, D49.4 — — — —

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
PPM001297 PSS000555|
European Ancestry|
7,622 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of bladder OR: 1.292 [1.201, 1.391]
β: 0.256 (0.0375)		 AUROC: 0.572 [0.55, 0.594] Nagelkerke's Pseudo-R²: 0.013
Brier score: 0.0917
Odds Ratio (OR, top 1% vs. Rest): 1.47 [0.779, 2.77]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE189.2_GWAS-Catalog-r2019-05-03-X189.2_PT_MGI_20200608

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
PSS000555 PheCode:189.2; ICD9CM:188.0, 188.1, 188.2, 188.3, 188.4, 188.5, 188.6, 188.7, 188.8, 188.9, 233.7, 236.7, 239.4, V10.51; ICD10CM:C67, C67.0, C67.1, C67.2, C67.3, C67.4, C67.5, C67.6, C67.7, C67.8, C67.9, D09.0, D41.4, D49.4 —
[
  • 789 cases
  • , 6,833 controls
]
 — European — MGI —