Childhood Cancer

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A comprehensive public resource for fusion-negative sarcoma sequencing data

University of California San Francisco
Alejandro Sweet-Cordero, MD & Richard Gorlick, MD
Grant Type: 
Crazy 8 Pilots
Year Awarded: 
Type of Childhood Cancer: 
Osteosarcoma, Rhabdomyosarcoma
Project Description: 

Fusion-negative sarcomas are a diverse and understudied subset of pediatric cancers. The most prevalent are embryonal rhabdomyosarcoma (ERMS) and osteosarcoma (OS). Osteosarcoma is characterized by an abnormal genome with many alterations, most of which are called “copy number gains” or “copy number losses.” In a normal genome, there are only two copies of every gene. However, in OS many genes have more than 4 copies, sometimes even 10 or more copies. ERMS is characterized by mutations in several targetable genes, commonly those in an altered pathway called the RAS pathway, as well as significant copy number gains. To date, several different groups have performed comprehensive sequencing of OS and ERMS. However, a significant barrier to progress in studying these tumors and in the design of novel precision medicine clinical trials is that it is not currently possible to visualize all of this data in one place because it is located in individual labs and in many separate databases. For example, it is quite difficult to evaluate how common a given copy number alteration in a specific gene is in either OS or ERMS. This inability to compare large data for these sarcomas limits our ability to identify recurrent or co-occurring alterations that might help us design better clinical trials. To address this significant problem, we propose to build a public resource that will allow for visualization and data sharing of all available ERMS and OS sequencing data.

Project Update - December 2020: A key limitation in advancing sarcoma research is to allow for increased data sharing between investigators. Specifically, for osteosarcoma and other pediatric sarcomas, there is a need for sharing of sequencing data that currently is located in many disparate repositories. To address this problem, we have established a new online portal for processing and sharing of sarcoma whole genome sequencing data. The portal uses a platform called cbiportal which is familiar to many cancer biologists. We anticipate that this portal will help other investigators interested in sharing sarcoma sequencing data and gaining insight about these rare disease.

Co-funded by: 
Northwestern Mutual Foundation