California Kids Cancer Comparison

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Principal Investigators

David Haussler, PhD, director, UC Santa Cruz Genomics Institute
Theodore Goldstein, PhD, director, MedBook

(L to R: Holly Beale; Jacob Pfiel; Katrina Learned; Geoff Lyle; Isabel Bjork; Olena Morozova; Sofie Salama; David Haussler; Ellen Kephart; Ann Durbin; Rob Currie)

Project Description

Each year 500 California children with cancer either lack or fail to respond to standard therapies. Clinical trials currently underway at UC Medical Centers are starting to employ genomic analysis to identify new therapies for these incurable tumors. So far these efforts yield new treatment possibilities for less than 10% of patients, in part because each tumor is analyzed on its own. 

The California Kids Cancer Comparison (CKCC) project provides the power of large-scale bioinformatics to improve this outcome. It analyzes each patient’s tumor in the context of thousands of pediatric and adult tumors that have undergone similar characterization. To help rapidly bring state-of-the-art analyses to our clinical collaborators, our team includes UC researchers and physicians in partnership with biotech and computer companies. Through the CKCC, we aim to at least double the number of kids that can benefit from a targeted cancer treatment. The concept can be scaled and applied to other genetic diseases and to all the 147,000 Californians diagnosed with cancer each year. 

As part of the CKCC project, we are developing MedBook, a social network designed for medical research and medical decision support. MedBook tools upload, manage and visualize both clinical and genomic data, handling this information in a manner protecting patient privacy. The tools process the genomic data using DNA genomic alignment, RNA sequence expression mapping, and pathway analysis, both at the cohort and the individual patient level. Clinicians and researchers will use MedBook to discuss and collaborate to find the best treatment for each patient, while patients and their advocates will be able to access this information and communicate with providers through this network.

Supplemental Project

We are now taking steps to advance our 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. 

Project Partners

Team Members

UC Santa Cruz

  • Robert Baertsch, PhD, MedBook Software Developer
  • Melissa Cline, PhD, Associate Project Scientist, Center for Biomolecular Science & Engineering 

  • Olena Morozova, PhD, Postdoctoral Scholar, Center for Biomolecular Science and Engineering
  • Sofie Salama, PhD, Research Associate, HHMI Senior Scientist, Center for Biomolecular Science & Engineering
  • Linda Rosewood, BA, Cancer Genomics Hub Program Director, Biomolecular Engineering

UC Irvine

  • Leonard Sender, MD, Director, Clinical Operations and Program Development & Division Chief, Pediatric Oncology, Chao Family Comprehensive Cancer Center, Clinical Professor Of Medicine School of Medicine

UC San Francisco

  • Sabine Mueller, MD, PhD, Director, Pediatric Brain Tumor Center

Stanford University

  • Alejandro Sweet-Cordero, MD, Associate Professor of Pediatrics

Children’s Hospital of Philadelphia

  • Adam Resnick, PhD, Assistant Professor of Neurosurgery

Collaborators

University of Southern California

  • Stephen Gruber, MD, PhD, MPH, Director, USC Norris Comprehensive Cancer Center; Professor of Medicine, Keck School of Medicine
  • Timothy Triche, MD, PhD, Professor of Pathology and Pediatrics

UC Davis

  • Marcio Malogolowkin, MD, Professor, Department of Pediatrics
    Chief, Division of Hematology Oncology

UC San Francisco

  • James Feusner, MD, Medical Director, Oncology, UCSF Benioff Children’s Hospital Oakland
  • Michael Prados, MD, Professor in Residence of Neurological Surgery; Director Translational Research in Neuro-Oncology
  • Trever Bivona MD, PhD, Associate Professor, Hematology and Oncology
  • Amit Sabnis MD, Post-doctoral Fellow, Pediatric Oncologist.
  • Elliot Stieglitz MD, Assistant Professor, Pediatrics
  • Benjamin Braun, MD, PhD, Associate Professor in Residence, Department of Pediatrics
  • Asmin Tulpule, MD, PhD, Clinical Fellow
  • Theo Nicolaides, MD, Assistant Professor, Pediatrics.

Industry and Nonprofit Partners

NuMedii

CISCO

DNAnexus

Translational Genomics Research Institute (TGen)

CARIS Life Sciences

Advocacy Partners

Unravel Pediatric Cancer 

Jacob’s Heart  

Kids v Cancer

Alex's Lemonade Stand Foundation

Team G Foundation

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