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Comparative Lesions Analysis Through a Targeted Sequencing Approach
Published on: November 5, 2019
Allelic imbalance analysis using a single-nucleotide polymorphism microarray for the detection of bladder cancer
Marieke J H Coenen1, Martine Ploeg, Mascha M V A P Schijvenaars
1Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
Summary
Single-nucleotide polymorphism (SNP) microarray analysis of urine shows limited effectiveness for detecting non-muscle-invasive bladder cancer recurrences. This method cannot replace current standard diagnostic procedures like cytology and urethrocystoscopy.
Area of Science:
- Urology
- Oncology
- Genetics
Background:
- Non-muscle-invasive bladder cancer (NMIBC) has a high recurrence rate.
- Current recurrence detection relies on cytology and urethrocystoscopy.
- Single-nucleotide polymorphism (SNP) arrays offer potential for noninvasive detection of genetic alterations.
Purpose of the Study:
- To investigate the suitability of SNP microarray analysis for detecting allelic imbalance in urine.
- To assess the utility of this method for identifying recurrences in NMIBC follow-up.
Main Methods:
- DNA from blood and urine of 158 NMIBC patients was analyzed using Affymetrix GeneChip Mapping 10K 2.0.
- Allelic imbalance was detected by comparing heterozygous SNPs in blood to homozygous SNPs in urine.
- Copy number changes were analyzed using Copy Number Analyser for GeneChip.
Main Results:
- Tumor-containing urine samples showed a higher frequency of allelic imbalance (0.4%) compared to non-tumor samples (0.04%).
- Copy Number Analyser for GeneChip identified significantly more copy number changes in tumor samples (P = 0.001).
- The diagnostic performance, measured by the area under the curve (0.67), indicated limited accuracy for recurrence detection.
Conclusions:
- SNP microarray analysis of urine allelic imbalance is not a reliable replacement for standard NMIBC recurrence detection methods.
- The method showed insufficient sensitivity and specificity for clinical application in NMIBC follow-up.