Our informatics work on cancer genomics provides a complete analysis pipeline from raw DNA reads through the detection and interpretation of mutations and altered gene expression in tumor samples. Our group collaborates with researchers at medical centers nationally—including members of the Stand Up To Cancer “Dream Teams,” the Cancer Genome Atlas (TCGA), and the International Cancer Genome Consortium (ICGC)—to discover molecular causes of cancer and pioneer a new personalized, genomics-based approach to cancer treatment.
I am co-founder of the Treehouse Childhood Cancer Initiative. The mission of the UC Santa Cruz Genomics Institute’s Treehouse Childhood Cancer Initiative is to change the story for childhood cancer patients by employing genomic data and computational approaches that could identify less toxic and more effective treatments. Treehouse analyzes a child’s cancer data against both childhood and adult patient cohorts across all types of cancer. This “pan-cancer” analysis of adult and pediatric tumors may identify situations where an adult drug is predicted to work on a subset of pediatric patients.
The UCSC Cancer Genomics Browser provides a new way to visualize and analyze data from studies aimed at improving cancer treatment by unraveling the complex genetic roots of the disease. The browser is a suite of web-based tools designed to help researchers find patterns in the huge amounts of clinical and genomic data being gathered in large-scale cancer studies. Medical researchers hope to identify genetic signatures and other “biomarkers” in cancer cells that can be used to predict how an individual patient will respond to different therapies throughout the course of their treatment.
The Haussler-Salama lab built the UCSC Cancer Genomics Hub (CGHub)—the first NIH Trusted Partner for distributing patient genomics data—to handle all the cancer genomics data generated by the large-scale genomics projects of the National Cancer Institute. The CGHub currently houses and analyzes all the large-scale data from the genomic programs of the National Cancer Institute. It is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from TCGA—a pioneering project involving more than 20 cancer types, from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project—which focuses on the five most severe childhood cancers—and from other related projects. The current planned capacity of this data center is five petabytes. We anticipate that the CGHub will serve as a platform to aggregate other large-scale cancer genomics information, growing to provide the statistical power to attack the complexity of cancer.
For more about the Haussler-Salama Lab’s work in cancer genomics, please visit the following project and program sites: Treehouse, UCSC Xena Functional Genomics Browser, BRCA Exchange, Cancer Gene Trust, and PRoTECT.