Fig. 1.

Flowchart depicting the methodological strategy employed in the current study. (A) Mouse gliomas were induced by PDGFB using RCAS/tv-a brain tumor models, after which cell lines are established and genomic DNA is extracted. (B) DNA fragments including the proviral sequence are pulled down using a hybridization probe capture protocol, sequenced, and mapped against the mouse genome. (C) Putative retroviral integration sites are detected as characteristic alignment peaks of softclipped reads. (D) The preliminary list of integration sites is filtered to remove potential false positive hits. (E) The integration direction of each retroviral insertion site is determined by analyzing the alignment of the softclipped read parts against the proviral sequence. (F) Integration sites are annotated against RefSeq genes. (G) Tagged, putative cancer genes are detected as common insertion sites across cell lines. (H) Tagged genes and loci are characterized in vitro and evaluated in the context of human GBM patient clinical data.