Exploring Current Challenges and Perspectives for Automatic Reconstruction of Clonal Evolution.

ABSTRACT

BACKGROUND/AIM: In the field of cancer research, reconstructing clonal evolution is of major interest. The technique provides new insights for analysis and prediction of tumor development. However, reconstruction based on mutational data is characterized by several challenges. MATERIALS AND METHODS: By performing extensive literature research, we identified 51 currently available tools for reconstructing clonal evolution. By analyzing two cancer data sets (n=21), we investigated the applicability and performance of each tool. RESULTS: Seventeen out of 51 tools could be applied to our data. Correct clustering of variants can be observed for 4 patients in the presence of ≤3 clusters and ≥5 time points. Correct phylogenetic trees are determined for 10 patients. Accurate visualization is possible, by applying adjustments to the original algorithms. CONCLUSION: Despite bearing considerable potential, automatic reconstruction of clonal evolution remains challenging. To replace tedious manual reconstruction, further research including systematic error analyses using simulation tools needs to be conducted.