Inactivation of the APC gene is considered the initiating event in human colorectal cancer. Modifier genes that influence the penetrance of mutations in tumor-suppressor genes hold great potential for preventing the development of cancer. The mechanism by which modifier genes alter adenoma incidence can be readily studied in mice that inherit mutations in the Apc gene. R encodes a recessive embryonic lethal mutation. We devised an exclusion strategy for mapping the Mom2 locus using embryonic lethality as a method of selection. Expression and sequence analyses of candidate genes identified a duplication of four nucleotides within exon 3 of the ␣ subunit of the ATP synthase (Atp5a1) gene. Tumor analyses revealed a novel mechanism of polyp suppression by Mom2 R in Min mice. Furthermore, we show that more adenomas progress to carcinomas in Min mice that carry the Mom2 R mutation. The absence of loss of heterozygosity (LOH) at the Apc locus, combined with the tendency of adenomas to progress to carcinomas, indicates that the sequence of events leading to tumors in Apc Min/+ Mom2 R/+ mice is consistent with the features of human tumor initiation and progression.[Supplemental material is available online at www.genome.org.]Colorectal cancer is one of the leading causes of cancer deaths in the United States (www.cancer.org). The dysregulation of normal colonic epithelium leads to the formation of adenomas, which are considered a prerequisite to progression to carcinoma (Fodde et al. 2003). This multistep process involves interactions between the genome and the gut environment, leading to mutations and epigenetic changes in oncogenes and/or tumor suppressor genes (Kinzler and Vogelstein 1996;Ilyas et al. 1999;Gregorieff and Clevers 2005). However, the variation in penetrance of hereditary forms of cancer has emphasized the impact of tumormodifier genes that can influence individual susceptibility to cancer by either enhancing or suppressing the initiation, growth, and/or progression of tumor cells. Due to environmental and genetic heterogeneity in the human population, it has been difficult to identify tumor modifier loci in humans. Therefore, complex trait analysis in experimental mouse crosses is a powerful approach to genetically dissect multigenic diseases (Moore and Nagle 2000;Threadgill et al. 2002;Siracusa et al. 2004).The mapping, identification, and characterization of genes influencing tumor susceptibility has been facilitated by the use of mammalian models (Mao and Balmain 2003). Inbred strains of mice that differ in their susceptibility to various types of solid tumors and leukemias have been instrumental in uncovering loci that affect tumor risk (Dragani 2003;Mao and Balmain 2003). Tumor susceptibility genes may act cell autonomously within the tumor lineage, or may act in a non-cell autonomous fashion within the microenvironment leading to tumor formation (Demant 2003). Genomic differences among inbred strains of mice are being exploited to limit the regions containing the causative allelic variants and ul...