N-Methyl-N′ ′ ′ ′-nitro-N-nitrosoguanidine (MNNG)-induced rat stomach carcinomas are considered to be a good model for differentiatedtype human stomach carcinomas. However, as for their molecular basis, only infrequent mutations of Catnb (β β β β-catenin) and Trp53 (p53) have been observed. Here, we carried out a whole-genome analysis of loss of heterozygosity (LOH) using 21 stomach carcinomas induced by MNNG in F 1 hybrids of ACI and BUF rats, and also analyzed promoter methylation of four tumor-suppressor genes. LOH analysis was performed using 130 polymorphic markers covering rat chromosomes 1-20 with an average interval of 20 Mbp. Despite adapting conditions so that LOH could be detected with up to a 50% contamination of stromal cells, no LOH was detected at any loci. CpG islands in putative promoter regions of four tumor-suppressor genes, Cdh1 (E-cadherin), Cdkn2a (p16), Mlh1, and Rassf1a, were analyzed by methylation-specific polymerase chain reaction (PCR). However, no methylation was detected. In contrast, the promoter region of Pgc (pepsinogen C), which lacks a CpG island, was methylated in all 21-cancer samples. These results indicated that LOH spanning a chromosomal region larger than 30 -40 Mbp or silencing of Cdh1, Cdkn2a, Mlh1, and Rassf1a, was not involved in MNNG-induced rat stomach carcinomas. The search for other genes involved in these carcinomas needs to be continued. (1) have proven to be good models for human differentiated-type gastric cancers.(2-5) Rat stomach cancers have histological features in common with human cancers, and closely reflect the effects of various tumor promoters, for example salt and sex hormones, and of preventive agents such as green tea components.(2-4) Based on oligonucleotide microarray analysis, it was found that rat stomach cancers had similar expression profiles to human stomach cancers; that is, genes involved in differentiated phenotypes of the stomach are downregulated, and genes involved in extracellular matrix remodeling and immune responses are upregulated. Clarification of molecular mechanisms in MNNG-induced rat stomach cancers is important for identifying novel molecular mechanisms in human stomach cancers. We have therefore worked to analyze genetic alternations in rat stomach cancers. With regard to the activation of oncogenes, Catnb (β-catenin) mutations were observed in high-grade lesions, although such lesions were infrequent (4/22).(6) Mutations of Kras2 (K-ras) and amplification of Fgfr2 (K-sam) and Erbb2 were not detected in 10 cancers, and are considered to be very infrequent.(7) With regard to the inactivation of tumor-suppressor genes, Trp53 (p53) mutations were infrequent (1/10), and microsatellite instability was absent. Regarding loss of heterozygosity (LOH), no information is available for rat stomach cancers, whereas frequent LOH has been observed in human stomach cancers.(8-10) Cancers induced in defined genetic and environmental conditions have limited sets of genetic alterations.(11-13) LOH analysis in MNNG-induced rat stomach cancer...