Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication
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Description
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".
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Copyright 2020 St. Jude Children's Research Hospital
Licensed under a modified version of the Apache License, Version 2.0 (the "License") for academic research use only; you may not use this file except in compliance with the License. To inquire about commercial use, please contact Xiaotu.Ma@stjude.org.
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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