Grant awarded to evaluate the effectiveness of comparative RNA-seq analysis within the clinical process

The California Initiative to Advance Precision Medicine (CIAPM) has awarded the Treehouse Childhood Cancer Initiative of the UC Santa Cruz Genomics Institute a follow-on California state grant worth $500,000. This award has been granted as a supplement to Treehouse’s work on the California Kids Cancer Comparison (CKCC) and focuses on a collaboration with Stanford University and Lucile Packard Children’s Hospital. State funding for this work is supplemented by local organization funding from St. Baldrick’s Foundation, Unravel Pediatric Cancer, local philanthropists Rafe and George Kraw, among others. Treehouse, the pediatric cancer research arm of the UCSC Genomics Institute was founded by its Scientific Director, David Haussler, and his former post-doctoral student, Dr. Olena Morozova.

“CKCC was a pilot project with ambitious goals for evaluating whether our big data analysis at the Genomics Institute can help kids being treated for cancer right now,” said Haussler. “We were able to make a convincing case that it works,” said Haussler. In this next stage of funding, “CKCC2” the UCSC Treehouse team will conduct 24-month registry study in collaboration with oncologists from Lucile Packard Children’s Hospital and Stanford Medical Center. This type of study collects and analyzes genomic data from a child’s cancer tumor, and presents this information to the treating clinical oncologist teams. CKCC2 will evaluate the effectiveness of comparative RNA-seq analysis within the clinical process, including assessing the impact on clinical decision-making, the patient and family understanding and engagement with genomic analysis, and tracking patient outcomes.

“For the CKCC2 project, we expect to work closely with Stanford clinical research staff using rigorous data-handling processes, institutionally approved protocols and consent forms,” said Isabel Bjork, Director of Pediatric Programs at the Genomics Institute. “We will have the ability to formally assess the clinical utility of genomic analysis within the clinical environment.”

In line with Treehouse’s commitment to providing open access to data, all software Treehouse uses is open source. This means that all RNA-seq processed data and accompanying analysis will be made publicly available to benefit researchers. The hope is that by maintaining open access, Treehouse can help advance the state of pediatric cancer research.

While Treehouse wants to know whether molecular-level tumor activity it has identified in the lab drives tumor growth, the team is ultimately concerned with whether genomic analysis could provide a measurable benefit to patients. Significantly, Treehouse proposes to measure “clinical benefit” not only in terms of tumor response and symptom control, but also in terms of how patients, their families and their physicians respond to this tool and use it into their decision-making. Information regarding acceptance of the genomic analysis will be useful in improving educational and training during widespread use of genomic-based precision medicine.

“At the end of the CKCC2 project, we will have a greater ability to evaluate whether Treehouse’s approach to precision medicine added value to the journey of the patients, their families and physicians,” said Haussler.

Source – Eurekalert

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