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Home > Organization > Divisions and Independent Research Units > Group for Frontier Science > Division of Rare Cancer > Research Projects > Establishment of fundamental research resource of rare cancer: Bioinformatics approach

Establishment of fundamental research resource of rare cancer: Bioinformatics approach

Rare cancer research has a unique problem; “the number of patients is small, and the clinical materials are hardly available for research”. Probably because the clinical materials are not well available for research, the fundamental research tools are not well developed for the rare cancer research. Division of Rare Cancer Research addresses this issue.

Bioinformatics approach

We can obtain the information about the events in our body by the experiments using clinical materials. The experiments using patient-derived cancer models are quite important for the translational research. However, the results and hypothesis should be validated by the experiments using clinical materials. Omics studies have been conducted in many types of malignancies, and the genetic aberrations relevant to metastasis, recurrence and resistance to treatments were reported. The data were deposited to the public database, and used in other studies. In rare cancers, the database can be improved in terms of construction and application.

We conduct the study on global genetic aberrations of rare cancers, and accumulate the data in our original rare cancer database. Our database will be opened and browsed on the websites. The database, which allows integrate the omics data with the clinical pathological information will promote the rare cancer research. For example, we constructed proteome database (References 1 and 2). Our proteome database, namely Genome Medicine Database of Japan (GeMDBJ Proteomics), was accessed by more than 600,000 times. As a database of disease proteomics, GeMBJ Proteomics is a unique research resource. Currently, we are constructing the database of transcriptome and genome of rare cancers.

The omics data of rare cancers have been generated using a small number of samples in many laboratories. Parts of the results are opened on line. Although the number of cases in individual studies is small, as a total, a considerable number of cases were subjected to the omics studies. We conduct meta-analysis of those data by integrating the data from academic papers. As the clinical materials for research are limited in the rare cancers, the use of existing omics data is especially required. The organization of clinical information of individual omics data sets and the application of bioinformatics are quite important for such studies. In Division of Rare Cancer Research, the researches with medical backgrounds curate the clinical and pathological information of cases for omics studies by reading academic papers, and register the results to our custom database. The data from in vitro cultured cell lines are also integrated to our analysis. We aim to develop the methodology to identify the innovative seeds for novel therapy.

In addition to biomarker development, the bioinformatics is useful for the study of re-localization of existing anti-cancer drugs to rare cancers. Using the aforementioned original database, we are developing the programs to identify the anti-cancer drugs for rare cancers in collaboration with Opt (http://www.opt.ne.jp/en/).