A new molecular diagnosis of stomach cancer determined by CGH and quantitative real time microsatellite analysis

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We detected the relative DNA copy numbers (RCNs) at the target loci in thirty patients with stomach cancer, with quantitative microsatellite analysis (QuMA), Seven microsatellite loci in chromosome 8q (D8S530,D851724,D851801) 16q (D1653140,D1653026) and 20q (D205911,D205185) and one gene specific locus (ZNF217) were selected as the target loci. The RCN was obtained relatively to a pooled reference cocsisting of six microsatellite promer sets selected from the regions where few aberrations have been observed in comparative genomic hybridization (CGH) analysis. Based on the TaqMan PCR system, internal probes used were carring donor (FAM) and acceptor (TAMRA) fluorescent molecules complementary to CA repeat in the microsatellite markers and to one gene specific oligomer in the gene specific marker. Chromosome 8q gain, 20q gain and 16q loss were detected in 18 (60%), 8 (26.7%) and 13 cases (43,3%), 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 (P0.0158), 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 hazard model, the double marker posive was a significant and independent factor indicationg an unfavorable prognostic factor (RR:17.176,95% Cl:2.782-106.026, P=0.0022). RCN aberrations in tumor tissues determined by QuMA enable to identify the prognostic factors that correlate with clinical outcome of the patients with stomach cancer.