Treehouse Childhood Cancer Initiative: Identification of Therapeutic Leads for Individual Pediatric Cancer Patients via Can-Cancer Analysis

Email Principal Investigator
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David Haussler

UC Santa Cruz Treehouse Childhood Cancer Initiative
Santa Cruz, CA, USA

CBTN Data Used


St. Baldrick's Foundation

California Initiative to Advance Precision Medicine

Unravel Pediatric Cancer

Team G Pediatric Cancer Foundation

Live For Others Foundation

Alex's Lemonade Stand Foundation for Childhood Cancer Research

American Association for Cancer Research

About this


The Treehouse Childhood Cancer Initiative research focuses on the value of tumor gene expression analysis using RNA sequencing for detecting aberrations in the genome and epigenome. The main objective of this project is to identify therapeutically actionable oncogenes with outlier expression in a patient’s tumor as compared to thousands of other pediatric and adult tumors, called the research compendia. The expression levels of the CBTN RNA-seq tumor data are included in the research compendia.

Ask The


Ask the scientists

What are the goals of this project?

Gather the expression data from as many pediatric and rare adult tumor types as possible to create gene expression tumor compendia available for pediatric cancer researchers worldwide, and to explore the utility of comparing an individual patient’s expression data to these tumor compendia.

What is the impact of this project?

This project is creating primary tumor, and cancer model compendia of thousands of uniformly processed tumor expression data derived from RNA-seq and is making them available to the research community. This project has also developed a comparative analysis of individual pediatric cancer patients’ gene expression data using the compendia.

Why the CBTN request is important to this project?

Including the CBTTC data in the research compendia is extremely important as pediatric brain cancer is rare and this many pediatric brain tumor data couldn’t be obtained elsewhere. Our comparative gene expression analysis compares a patient’s tumor to the most similar tumors in the compendia. The inclusion of CBTTC data in the compendia significantly improves our ability to analyze pediatric brain tumor patient data



Results are still in progress. So far the compendia contain gene expression data for nearly 13,000 tumors in total, over 3,000 of which are from pediatric or young adult patients. We have demonstrated the feasibility of our comparative RNA-seq analysis in a clinical setting, and showed that potentially actionable findings in pediatric cancer cases increase when RNA-seq data is considered

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


Meet The


Holly Beale, Senior Bioinformatician

Isabel Bjork, Program Manager

Allison Cheney, Ph.D. student

David Haussler, Scientific Director

Ellen Kephart, Software Engineer

Katrina Learned, Data Coordinator

Alfred G. Lyle, Data Analyst

Olena Morozova, Scientific Lead

Sofie Salama, Research Scientist

Lauren Sanders, Postdoctoral Researcher

Anouk van den Bout, Lab Manager