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(Variants and weights)

Polygenic Score (PGS) ID: PGS000071

Predicted Trait

Reported Trait: Bladder cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): bladder carcinoma

Score Details

Name: CC_Bladder

Original Genome Build: GRCh37
Number of Variants: 15

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002243
PubMed: 24163127
18,729 individuals European
PubMed: 26732427.0 301,328 individuals
[ 15,058 cases, 286,270 controls]
European
GWAS Catalog: GCST001153
PubMed: 21750109
43,837 individuals European
(Netherlands)
GWAS Catalog: GCST002460
PubMed: 24861552
91,850 individuals European
GWAS Catalog: GCST000842
PubMed: 20972438
8,652 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000191 PSS000110 Graff RE et al. (2020) 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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 412,602 individuals
[ 2,248 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB