University of Hawaiʻi Cancer Center researchers developed a computational algorithm to analyze “big data” obtained from tumor samples to better understand and treat cancer.
“A growing problem in cancer research is figuring out how to analyze the many kinds of big genomic data for different cancers,” said Gordon Okimoto, co-director of Biostatistics and Informatics Shared Resource at the UH Cancer Center. “The overwhelming quantity and complexity of the data has created an analysis bottleneck that has slowed the translation of the knowledge within the data to the clinic.
“We have figured out a way to mine these data for the benefit of cancer patients.”
Okimoto and collaborators developed a computational algorithm called the Joint Analysis of Many Matrices by ITeration (JAMMIT). JAMMIT uses advanced mathematics to identify different patterns across multiple molecular data types such as gene expression and genetic mutations that when taken together accurately predicts what treatments would be best for a given cancer patient.
“The algorithm could accelerate the approval of powerful treatments for many cancers, improve clinical outcomes, and reduce costs for treating cancer,” said Randall Holcombe, incoming director of the UH Cancer Center. “I believe this discovery can open a path to more precision medicine clinical trials that could be initiated and run locally in Hawaiʻi.”
Algorithm use on liver and ovarian cancer
The findings published in Biodata Mining highlight JAMMIT analysis of ovarian and liver cancer data pulled from private research labs and public databases such as The Cancer Genome Atlas, a National Cancer Institute data archive. The analysis identified small sets of genes that accurately predict which patients would benefit most from chemotherapy. These same signatures also suggest that many of the ovarian and liver cancer patients studied would benefit from combining chemotherapy with immunotherapy.
Okimoto plans on analyzing the data for dozens of more cancers.
The liver cancer results were based in part on tissue samples collected locally by the liver cancer working group (TeamLiver). TeamLiver includes about 15 researchers and physicians from the UH Cancer Center and local hospitals that make up the Hawaiʻi Cancer Consortium collaborating on liver cancer research for more than 4 years. Hawaiʻi has one of the highest rates of liver cancer in the nation and the second highest liver cancer mortality rate in the U.S. (Hawaiʻi Cancer Facts and Figures).
Startup based on JAMMIT technology
Okimoto and Thomas Wenska started SNR Analytics, Inc. The start-up is focused on securing the IP and funding for the development of a computational pipeline based on the JAMMIT algorithm for the discovery of predictive gene signatures for cancer and other complex diseases.
—By Nana Ohkawa