Polygenic Score (PGS) ID: PGS000071

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) urinary bladder carcinoma (MONDO_0004986)
Released in PGS Catalog: Feb. 12, 2020
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name CC_Bladder
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 15
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
464,396 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002243
Europe PMC: 24163127
 18,729 individuals European 16 cohorts
  • ATBC
  • ,BBCS_b
  • ,CPSII
  • ,EAGLE
  • ,EPIC
  • ,FPCC
  • ,FrBCS
  • ,HPFS
  • ,LABCS
  • ,MEC
  • ,NEBCS
  • ,NHS
  • ,PLCO
  • ,SpBCS
  • ,TXBCS
  • ,WHI
Europe PMC: 26732427
[
  • 15,058 cases
  • , 286,270 controls
]
 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
GWAS Catalog: GCST000842
Europe PMC: 20972438
 8,652 individuals European NR

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
PPM000191 PSS000110|
European Ancestry|
412,602 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 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
PPM002037 PSS001010|
European Ancestry|
391,888 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident blader cancer HR: 1.28 [1.2, 1.37] AUROC: 0.803
C-index: 0.813 (0.008)		 — Age at assessment, sex, genotyping array, PCs(1-15), cigarette pack-years, smoking status(never vs. former vs. current), body mass index C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017172 PSS010143|
European Ancestry|
424 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Bladder cancer HR: 1.21 [1.1, 1.33] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index —

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
PSS010143 — —
[
  • 31 cases
  • , 393 controls
]
 — European — UKB —
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
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
PSS001010 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 890 cases
  • , 390,998 controls
]
 — European — UKB —