Polygenic Score (PGS) ID: PGS000071

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) bladder carcinoma (EFO_0000292)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name CC_Bladder
Variants
Original Genome Build GRCh37
Number of Variants 15
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002243
EuropePMC: 24163127
18,729 individuals European
GWAS Catalog: GCST001153
EuropePMC: 21750109
43,837 individuals European
(Netherlands)
GWAS Catalog: GCST002460
EuropePMC: 24861552
91,850 individuals European
GWAS Catalog: GCST000842
EuropePMC: 20972438
8,652 individuals European
EuropePMC: 26732427
[
  • 15,058 cases
  • , 286,270 controls
]
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
PPM000191 PSS000110 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Bladder cancer OR: 1.3[1.25, 1.36] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

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
PSS000110 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 29010
[
  • 2,248 cases
  • , 410,354 controls
]
,
0.46 % Male samples
Mean = 58.0 years European GERA, UKB