Related Experiment Video
Updated: Aug 24, 2026
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Comparative study between DNA copy number aberrations determined by quantitative microsatellite analysis and clinical
Seiji Suzuki1, Kaku Egami, Koji Sasajima
1Department of Surgery, Tama-Nagayama Hospital, Nippon Medical School, Tama-Shi, Tokyo, Japan. seiji@nms.ac.jp
Purpose:
We detected the relative DNA copy numbers (RCNs) at target loci in patients with stomach cancer with quantitative microsatellite analysis. We additionally clarified the relationship between DNA copy number aberrations and the clinical outcome of the patients.
Experimental Design:
Fresh frozen samples were obtained from 30 patients who had undergone surgery for stomach cancer. Seven microsatellite loci in chromosomes 8q, 16q, and 20q and one gene-specific locus (ZNF217) were selected as the target loci. The DNA copy number was obtained relatively to a pooled reference consisting of six microsatellite primer sets selected from the regions where few aberrations have been reported in comparative genomic hybridization analysis. On the basis of the TaqMan PCR system, the internal probes used were carrying donor (6-carboxyfluorescein) and acceptor (6-carboxytetramethylrhodamine) fluorescent molecules complementary to CA repeats in the microsatellite markers and to one gene-specific oligomer in the gene-specific marker.
Results:
Chromosome 8q gain, 20q gain, and 16q loss were detected in 18 (60.0%), 8 (26.7%), and 13 (43.3%) cases, respectively. Gains in the RCNs of D8S1801 and D8S1724 were most frequently found (36.7%). There was a significant correlation between the loss of D16S3026 and reduced survival duration (P = 0.0158), and the simultaneous aberrations of D8S1801 gain and D16S3026 loss (double marker positive) was significantly associated with reduced survival duration (P = 0.0008). According to Cox proportional hazards model, the double marker positive was a significant and independent factor indicating an unfavorable prognostic factor (relative risk, 17.176; 95% confidence interval, 2.782-106.026; P = 0.0022).
Conclusion:
RCN aberrations in tumor tissues determined by quantitative microsatellite analysis enable identification of the prognostic factors that correlate with clinical outcome of the patients with stomach cancer.
Insights
DNA copy number aberrations in stomach cancer patients, identified through quantitative microsatellite analysis, are linked to survival outcomes. Specific genetic alterations, like D8S1801 gain and D16S3026 loss, serve as significant prognostic indicators.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Stomach cancer exhibits complex genetic alterations.
- Understanding DNA copy number variations is crucial for predicting patient prognosis.
Purpose of the Study:
- To detect relative DNA copy numbers (RCNs) at target loci in stomach cancer patients.
- To investigate the correlation between DNA copy number aberrations and clinical outcomes.
Main Methods:
- Quantitative microsatellite analysis was performed on fresh-frozen tumor samples from 30 stomach cancer patients.
- Seven microsatellite loci and one gene-specific locus (ZNF217) were analyzed using a TaqMan PCR system.
- DNA copy numbers were relatively quantified against a reference pool.
Main Results:
- Chromosome 8q gain (60.0%), 20q gain (26.7%), and 16q loss (43.3%) were frequently observed.
- D8S1801 and D8S1724 RCN gains were most common (36.7%).
- Loss of D16S3026 and combined D8S1801 gain/D16S3026 loss significantly correlated with reduced survival (P=0.0158 and P=0.0008, respectively).
Conclusions:
- Relative DNA copy number aberrations in stomach tumors can be identified using quantitative microsatellite analysis.
- These aberrations serve as significant prognostic factors for stomach cancer patients.
- Combined D8S1801 gain and D16S3026 loss is an independent unfavorable prognostic factor.
