Detecting Gene Fusions and Subtype Discovery in Pediatric Solid Tumors RNA-Seq using CICERO

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CBTN Data Used


St. Jude Cloud project core funding

About this


The proposed study will be an exploratory examination of fusions and expression in pediatric tumors including neuroblastoma, low and high grade glioblastoma, medulloblastoma, choroid plexus carcinoma, ependymoma and other rare diagnoses. St. Jude has RNA seq from approximately 1200 brain tumor patients to include in the study.

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What are the goals of this project?

The goals of this project are to improve the accuracy of frequency estimates of rare and unique gene fusions in the pediatric brain tumor population by tabulating the harmonized results of fusion detection calls on CBTN samples data with St. Jude RNA seq samples, to discern novel subtypes of pediatric tumors by combining fusion detection calls and harmonized source corrected expression values within general brain tumor diagnoses and to prioritize detectable fusions for future study by combining the improved frequency detection, cluster definition and any longitudinal clinical covariates that may indicate a sub class of tumors that could benefit from distinct treatment.

Why the CBTN request is important to this project?

The rarity of tumor samples from many subtypes of pediatric neurological cancers has limited our ability to confidently predict the population frequency of uncommon or unique gene-fusions. Analyzing the RNA seq data from CBTN brain tumor samples would improve our estimates of gene fusion frequency so that leads could be more effectively prioritized. Further after adjusting for batch effects, clustering RNA seq expression vectors from a combined population of St. Jude and Kids First samples will improve our power and sensitivity to potentially discern novel subtypes for rare tumors that may lead to more precise personalized treatment. Last our goal is to bring our CICERO fusion detection method to the data by developing a workflow for CAVATICA in order to harmonize the analysis of CBTN samples with those from St. Jude and to gain experience in federated analysis.

Specimen Data

The Children's Brain Tumor Network contributed to this project by providing access to the Pediatric Brain Tumor Atlas

Explore the data in these informatics portals