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Transcriptome-wide association study identifies genes associated with bladder cancer risk
Siting Li1,2, Jiang Gui1, Margaret R Karagas2
1Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
Scientific Reports
|January 9, 2025
Summary
This study used transcriptome-wide association studies (TWAS) to link gene expression to bladder cancer risk. Four genes, SLC39A3, ZNF737, FAM53A, and PPP1R2, were identified as significantly associated with bladder cancer development.
Area of Science:
- Genetics
- Oncology
- Bioinformatics
Background:
- Genome-wide association studies (GWAS) have identified genetic variants linked to bladder cancer susceptibility.
- However, the role of gene regulation in bladder cancer development remains largely unexplored.
Purpose of the Study:
- To investigate the association between genetically predicted gene expression and bladder cancer risk.
- To extend existing GWAS findings by exploring the functional impact of gene regulation.
Main Methods:
- A transcriptome-wide association study (TWAS) was performed using PrediXcan.
- Gene expression levels were predicted in whole blood using genome-wide genotype data from 6180 bladder cancer cases and 5699 controls.
- Logistic regression analysis was employed to assess gene-level associations with bladder cancer risk, adjusting for relevant covariates.
Main Results:
- TWAS identified four genes significantly associated with bladder cancer risk: SLC39A3 (OR=0.91), ZNF737 (OR=0.91), FAM53A (OR=1.09), and PPP1R2 (OR=1.09).
- Associations were evaluated using false-discovery rate (FDR) correction to control for multiple testing.
- Individual single-nucleotide polymorphisms (SNPs) and proximal loci were further assessed.
Conclusions:
- Genetically regulated gene expression plays a role in bladder cancer development.
- The identified genes (SLC39A3, ZNF737, FAM53A, PPP1R2) represent potential targets for bladder cancer prevention and treatment strategies.
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