Our Major Goals

Structural variants (SVs) as well as extrachromosomal circular DNA (ecDNA) are known drivers of aggressive tumor growth by promoting oncogenic fusion genes and high oncogene copy number. Analysis of the effects of SVs on the gene regulatory landscape of tumor genomes as well as profiling the frequency and diversity of ecDNA in the different types of pediatric brain tumors are currently the focus of research in the Chavez lab.

Recently, we have demonstrated how to leverage epigenetic information such as DNA methylation and enhancer profiling in pediatric brain tumors and normal human tissues to identify clinically relevant tumor subgroups, oncogenic enhancers, transcription factors, and pathways amenable to pharmacologic targeting. To reveal regulatory circuitries disturbed in childhood brain tumors, the lab generates and integrate public high-dimensional data from primary tumors and patient-derived models. By integrating these heterogeneous data types, we aim to identify oncogenic mechanisms and novel tumor-dependency genes and pathways that may provide new targets for improved therapeutic approaches. In addition, the lab develops and applies new statistical and machine learning tools for the quantitative and integrative analysis of heterogeneous genetic and epigenetic data.

NEW: Check here for our latest preprints on The landscape of extrachromosomal circular DNA in medulloblastoma and Oncogenic 3D genome conformations in ependymoma.