A comprehensive analysis of genome integrity during neoplastic growth in Drosophila using overlapping paired-end reads and a Deterministic Structural Variation Detection algorithm. Drosophila melanogaster

The development of cancer has been associated with the gradual acquisition of distinct hallmark character- istics leading to a progressive increase in malignancy. Qualified genome instability is generally considered a precondition for the onset of this process; however, a comprehensive understanding of its contribution is still missing. To assess the importance of genome stability during tumorigenesis in Drosophila melanogaster, we induced tumor formation by knockdown of the Polycomb group (PcG) tumor suppressor polyhomeotic and investigated genome integrity by the performance of genome sequencing. For a highly resolved genome structure analysis we developed the Deterministic Structural Variation Detection (DSVD) algorithm, which identifies structural variations (SVs) with high accuracy and at single base resolution. The employment of long overlapping paired-end reads enables DSVD to perform a deterministic, i.e. fragment size distribution independent, identification of discordant read pairs and to cover a larger size spectrum of SVs. Practical application of DSVD to our sequencing data reveals a substantial genetic variation with respect to the ref- erence genome, similarly identified in the control and the tumor, reflecting the temporal separation of the reference and our laboratory strains. The majority of all SVs, constituted by small insertions/deletions and strongly enriched within non-coding regions, are potentially caused by erroneous replication or transposition of mobile elements. Altogether, our results demonstrate that genome integrity is not affected inevitably during sustained tumor growth in Drosophila implying that tumorigenesis can occur irrespective of genome stability and accumulation of genetic alterations in this model organism.