Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication

Oncogenic fusions formed through chromosome rearrangements are hallmarks of childhood cancer that define cancer subtype, can provide prognostic value, remain stable upon treatment or during clonal evolution and have a high potential for serving as novel therapeutic vulnerabilities. However, mechanistic understanding of the etiology of oncogenic fusions in childhood cancers remains elusive.

In order to better study these questions, we developed several methods, including neoversioner to study fusion version patterns, neosplicer to detect neosplicing sites for a given fusion, DNA breakpoint detection based on RNAseq data and CRIPSR processing code.  Prerequisite tools are listed in "manifest.docx" and and reference files can be generated following "download_reference.sh".

Run command can refer README file and "example.sh". We also included all edited fastq files under CRISPR folder. All steps processing CRIPSR sequence data are included in file "CRISPR/cri-splicer.sh". All Figures included in the study and their according codes are available in folder "Figures/jobs.sh".