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Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Cell-Free DNA Integrity Analysis in Urine Samples

Cell-Free DNA Integrity Analysis in Urine Samples

Published on: January 5, 2017

Identification of Genetic Risk Factors for Familial Urinary Bladder Cancer: An Exome Sequencing Study.

Alexander Pemov¹, Talia Wegman-Ostrosky¹, Jung Kim¹

¹Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD.

JCO Precision Oncology

|December 29, 2021

Summary

Genetic predisposition to urinary bladder cancer (UBC) is complex. This study identified genetic variants in DNA repair, cilia, and metabolism pathways, suggesting polygenic inheritance for UBC risk.

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Area of Science:

Genetics
Oncology
Molecular Biology

Background:

A family history of urinary bladder cancer (UBC) suggests a genetic component, but known genetic risk factors are incomplete.
Previous studies indicate a significant genetic predisposition to UBC, yet the underlying genetic architecture remains largely undefined.

Purpose of the Study:

To identify novel genetic variants and pathways associated with familial urinary bladder cancer (UBC) risk.
To investigate the genetic basis of UBC predisposition in multiplex pedigrees and familial cases.

Main Methods:

Exome sequencing of patients from UBC pedigrees and familial UBC cases.
Analysis of pathogenic germline variation in candidate genes within The Cancer Genome Atlas (TCGA) UBC cohort.
Comparison of variant frequencies between UBC cases and cancer-free controls.

Main Results:

Identified familial-specific variants clustering in DNA repair (MLH1, MSH2) and cellular metabolism (IDH1, ME1) pathways.
Significantly higher burden of pathogenic/likely pathogenic variants in familial UBC cases compared to controls (P = .003).
Increased pathogenic variant load observed in genes related to cilia biogenesis (P = .001).

Conclusions:

Urinary bladder cancer predisposition is complex and likely polygenic.
Identified genetic variants implicate DNA repair, cilia biogenesis, and cellular metabolism pathways in UBC etiology.
Further research is needed to elucidate the role of specific genes like CHEK2 in UBC development.