Martin Strauch- Seminar ”Selected Topics in Bioinformatics”

It has been observed that cancer genomes typically show not only an increased rate of single nucleotide mutations but also an increase in the number of genome rearrangements. As sequencing whole genomes is still a time-consuming task a method has been proposed for reconstructing the cancer genome from the known sequence of the human genome by finding the breakpoints alongside which the rearrangements occurred. The method involves end sequence profiling (ESP) of the cancer genome which is available in BAC library vectors. Mapping the end sequences to the human genome, the candidates for the breakpoints can be identified. For the reconstruction of the cancer genome G ’ the events have to be found that rearrange the human genome G into G’. This task is specified in the definition of the ESP Genome Reconstruction Problem [ESPGRP] and, additionally, a heuristic approach providing a solution will be given. Finally, the method is applied the MCF7 breast cancer genome resulting in a map of the rearranged cancer genome. This work is based in large parts on an article by Raphael et al. (2003), accompanie