In past reporting periods, we procured a series of primary endometrial carcinosarcomas and paired non-tumor tissues through the Cooperative Human Tissue Network, which is supported by the National Cancer Institute. We then: 1. Subjected a subset of the tumor-normal pairs to whole exome sequencing at the NIH Intramural Sequencing Center. 2. Curated and filtered the exome sequence data to distinguish germline variants (present in both tumor and normal DNAs) from somatic variants (present exclusively in the tumor DNA). 3. Subjected the somatic variants to orthogonal validation, using Sanger sequencing and/or mass spectrometry, to distinguish true somatic mutations from false-positive calls. 4. Prioritized a subset of nonsynonymously, somatically mutated genes for further analysis in a mutation prevalence screen. During the current reporting period, we: 1. Completed the first phase of a mutation prevalence screen. In this screen we PCR-amplified and Sanger-sequenced the subset of prioritized genes, which we hypothesize are likely to be causal cancer genes, from an independent cohort of endometrial carcinosarcomas. We subsequently analyzed the sequence data to identify potential somatic (tumor-specific mutations). We subsequently performed an independent PCR-amplification and sequencing of potential somatic mutations to confirm whether they were true positives. In the incoming reporting period we plan to: 1. Determine the so-called coverage of the mutation prevalence screen in order to identify any sequence gaps. 2. If necessary, increase the coverage of the prevalence screen by sequencing over any gaps. 3. Define the mutation frequency, and mutation spectrum of the genes in the prevalence screen. 4. Use statistical methods to determine whether any of the genes in the mutation prevalence screen are so-called significantly-mutated genes, i.e. whether they are mutated at a statistically significantly higher rate than the background mutation rate for endometrial carcinosarcomas. We hypothesize that significantly-mutated genes are likely to be causal cancer genes that contribute to the development of endometrial carcinosarcomas. 5. Analyze the whole exome sequence data to identify somatic copy number alterations in endometrial carcinosarcomas. 6. Prepare a manuscript describing the results of this project.
