California Kids Cancer Comparison

Principal Investigator

David Haussler, PhD
Director, Genomics Institute; UC Santa Cruz

Project Background

Pediatric cancer

Compared to 50 years ago, standard treatment for childhood cancer has remained largely unchanged. In California, 500 of the 1,700 children annually diagnosed with cancer either do not respond to standard treatments or have no standard therapies available to treat their condition. Hard-to-treat cancers are categorized as "relapsed" or "refractory," meaning they have resisted available treatments. For most of these patients, hospice is the only remaining option.

Whereas adult cancers are often linked to genetic mutations that are acquired during an individual’s lifetime, such as through environmental exposures, pediatric cancers present with fewer mutations and are therefore more difficult to diagnose. Support for and advancement of adult cancer therapies continue to progress compared to pediatric cancers, due in large part to ample federal funding, the underlying biology of adult cancers, more established data sharing platforms, and the drug development pipeline. Childhood cancers are significantly less common, which ultimately limits clinical trials from recruiting sufficient numbers of patients and makes drug development a much slower process than for adult cancers. Pediatric cancers also tend to be more complex, which prevents a single therapy from benefitting large groups of patients. Of federal funding allocated to the National Cancer Institute, approximately 4% is annually designated for pediatric cancers.

DNA-based therapies

Cancer cells are characterized by uncontrolled cell growth that causes tumors to form and grow. This occurs because the cancer cells’ genome (complete blueprint of genetic material, or DNA) has acquired specific mutations (changes in basic DNA units). Until 2017, cancer drugs were developed to target specific mutations based on where a tumor was located within the body (e.g., lung cancer). These targeted drugs work by interfering with the ability of cancer cells to grow or survive. They are effective as long as the patient’s tumor has the most common mutation the drug is designed to target. Occasionally, a mutation known to occur in one tumor type is detected in a tumor in a different location of the body. For instance, a mutation typically found in lung cancer may be found in a brain tumor. Since the drug is targeted to prevent or reverse the negative effects of that mutation, it may help treat the brain cancer, even though it was originally developed for lung cancer. With access to advanced DNA sequencing technologies, the details of each person’s cancer can help direct the treatment strategy.

RNA-based therapies

Just as in healthy cells, each cancer cell contains the full genome but only uses a fraction of the total available genes to perform its specialized functions. Which genes are active or dormant distinguishes one cell type from another, like a muscle cell compared to a kidney cell. Scientists can uncover which genes are active by identifying the collection of RNA molecules present in a cell, which are single-helix copies of double-helix DNA. Consider the analogy of DNA as the full set of blueprints of a building site and RNA as the daily orders for a construction crew. The set of RNA molecules present in a cell is known as its 'transcriptome,' and the scientific field is called 'transcriptomics.' By comparing RNA molecules that are detected in a patient's tumor to those found in thousands of other tumors (comparative RNA analysis), scientists can ascertain how the molecular pattern of a patient's tumor resembles or differs from other tumors. This information can help guide the best treatment strategy based on the underlying mechanisms of tumor growth.

Project Summary

For hard-to-treat cancers, recent clinical trials based on tumor genomics have had limited success, especially for children. On average, DNA analysis of pediatric cancers yields useful information for fewer than 10% of patients for whom standard treatment has been unsuccessful. The California Kids Cancer Comparison (CKCC) project sought to ameliorate cancer care for pediatric patients by leveraging two fundamental concepts: 1) instead of relying exclusively on genomic mutations in the tumor (DNA-based analysis), the research team employed an RNA-based approach; and 2) the team instituted large-scale computation to compare all RNA in a specific tumor with over 11,000 tumors from other patients (“Cancer Comparison”). Using these techniques, the team aimed to determine what is likely driving the uncontrolled growth of a patient’s specific tumor and therefore identify new potential targets for therapy.

As a step toward incorporating RNA analysis in the clinic, the research team collaborated with ongoing clinical trials for children with cancer. While the trials looked for new treatment options based on tumor DNA, CKCC obtained each tumor’s RNA data and analyzed it in several innovative ways. Using this data-driven comparative approach, the team identified new molecular information about the case, previously unavailable to the clinical team, in 100% of cases, exceeding their original goal of 20% for this initial study. Some of this information could be used for alternative treatment possibilities. The team then communicated its findings to the clinical trials and received feedback to develop effective communication strategies with clinicians.

To further test clinical efficacy of comparative cancer RNA analysis, the research team established a registry focused on clinical validation of the findings and optimization of patient/family engagement in medical decision-making. Supported by external funds, this work is ongoing and will be completed by the end of 2019.

Supplemental Project

The team took steps to advance their data-driven tumor analysis toward clinical testing by evaluating the effectiveness of comparative RNA-sequencing analysis within the clinical process, including assessing: the impact on clinical decision making, the patient family understanding and engagement with genomic analysis, and patient outcomes. In line with UCSC’s commitment to providing open access to data, all software developed by UCSC genomic researchers for CKCC is open source. This means that all RNA-sequencing processed data and accompanying analysis will be made publicly available to benefit researchers. The hope is that by maintaining open access, CKCC can help advance the state of pediatric cancer research.


Research Team and Collaborators

UC Santa Cruz

  • Olena Morozova Vaske, PhD
  • Isabel Bjork, JD, MSc, MA
  • Rob Currie, MBA
  • Holly Beale, PhD
  • Ted Goldstein, PhD
  • Ann Durbin
  • Katrina Learned
  • Ellen Kephart
  • Jacob Pfiel
  • Lauren Sanders
  • Katrina Slater

Stanford University, Lucile Packard Children's Hospital

  • Sheri L. SPunt, MD, MBA
  • Norman J. Lacayo, MD
  • Kara L. Davis, DO
  • Alejandro Sweet-Cordero

UC San Francisco

  • Alejandro Sweet-Cordero
  • Sabine Mueller

University of British Columbia, BC Cancer Agency

  • Marco Marra

Children's Hospital Orange County

  • Leonard Senders
  • Ashley Plant

Children's Mercy Hospital in Kansas City

Sanford University of South Dakota Medical Center

University of Michigan

University of Pittsburg

Alex's Lemonade Stand Foundation

Amazon Services


Jacob's Heart

Key for a Cure

Kids v Cancer

Live For Others Foundation

St. Baldrick's Foundation

Team Finn

Team G Foundation

Unravel Pediatric Cancer




Seven Bridges

George Kraw

Project team photos

Holly Beale; Jacob Pfiel; Katrina Learned; Geoff Lyle; Isabel Bjork; Olena Morozova; Sofie Salama; David Haussler; Ellen Kephart; Ann Durbin; Rob Currie

Project Leverage

In order to achieve its goals, the CKCC project requires additional funds and resources beyond those provided by CIAPM. The state’s contribution to the project is significantly leveraged by the fact that CKCC acquires genomic data generated by its clinical trial partners (Stanford University, UC Irvine, UC San Francisco) at no cost to CKCC, which represents a total of over $16.5 million in clinical trial funding.

Portions of several currently funded projects and personnel at UC Santa Cruz and patient advocacy groups contribute over $1.2M to CKCC.

The CKCC team has attracted significant follow-on funding for their project, and is supported since July 2016 by a $2.5 million 5-year grant from the St. Baldrick's Foundation to continue their work on finding more treatment options for kids with cancer.

Additional Contributions

UCSC provided in-kind support through administrative fees and faculty time