We have previously performed a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer (Groebner et al., Nature 2018 https://www.ncbi.nlm.nih.gov/pubmed/29489754). Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analyzed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copynumber variant (correlating with germline variants). We have now developed new and improved tools for the analysis of whole genome sequencing data.
What are the goals of this project?
We aim to perform a similar pediatric pan-cancer analysis focused on the discovery of structural variants and other genomic rearrangements using our new tools. We intend to install our tools as docker containers to the St. Jude cloud and analyze all available whole genome sequencing data. Our tools use CNV information as seeds. Identified events will be analyzed for their effects on gene expression by integrating gene expression data.
The Children's Brain Tumor Network contributed to this project by providing access to the Pediatric Brain Tumor Atlas.