The Cancer Genome Atlas: More Than a Large Collection of Data
December 7, 2015, by Jean Claude Zenklusen, Ph.D.
After collecting samples from more than 11,000 patients across 33 tumor types, and generating a vast, comprehensive data set to describe the molecular changes that occur in cancer, The Cancer Genome Atlas project is coming to a close. Tissue sample collection and data generation are completed. Eighteen integrative analyses of individual cancer types have been published and the analyses for another fifteen papers are underway.
However, though TCGA will wrap up in 2016, cancer genomics projects built upon the success of TCGA will continue to play a major part in the NCI’s mission to better understand and treat cancer in the years to come.
Transforming Cancer Research
The value of the TCGA data set cannot be overstated. Its richness has enabled researchers to define a more meaningful taxonomy of cancer types and subtypes, uncover patterns across related tissue types through pan-cancer analysis, and even investigate questions that were not imagined at the outset of the project, such as the mining of the data to discover new viruses and other microbial agents. The TCGA research network maker papers, comprehensive cross-platform analyses of TCGA data on each cancer type, serve as additional resources for understanding the molecular features of these cancers.
While the TCGA data and research network analyses will continue to serve the community, the greatest impact of TCGA has been its transformation of the way cancer genomics is conducted. By advancing three main areas of cancer genomics research, TCGA has enabled current and future projects to far surpass the scope of TCGA:
- Team Science
TCGA has shown that the integrative, cross-platform, interdisciplinary investigation made possible by scientific consortia is extremely valuable. Further, many scientists have built a successful academic career through participation in TCGA, demonstrating that the model of scientific collaboration gives researchers the opportunity to receive academic credit and recognition. Thanks to TCGA, the model of team science will continue to thrive, benefiting science as well as the scientists.
- Genomic Data Analysis Pipelines
TCGA honed its methods for tissue sample collection and selection, genomic data production, and genomic data analysis over the course of a decade. The pipelines, standards, and best practices that TCGA developed have become invaluable resources for the research community and will continue to serve as the backbone for future genomic research projects.
- Sample Acquisition and Preservation
TCGA has been instrumental in highlighting the need for thoroughly annotated, high quality tumor samples with matched normal controls and informed consent from the patient. The NCI now requires that clinical trials follow a set of standard practices to make high quality tissue samples available for researchers. These improvements in clinical trial design and organization greatly facilitate the integration of cancer genomics and clinical cancer research.
Paving the Way for Clinically-Oriented Cancer Genomic Studies
Each of these advances in the way genomic science is conducted has laid the groundwork for CCG’s new projects, which seek to answer the question, “What can genomics tell us about the clinical features of cancer?”
CCG projects like Clinical Trials Sequencing Project, Cancer Driver Discovery Program, and Exceptional Responders utilize samples of tumor and paired normal tissue from clinical trials and medical practices to investigate why some patients respond to treatment and others do not, and why some patients are cured and others relapse. While these projects are still in their early phases, the preliminary results are promising. In the Exceptional Responders project, several of the tumors that have been analyzed to date contain an evident genomic explanation for the exceptional response to treatment.
This link between genomics and clinical outcome is a promising prognostic for the application of genomics to cancer. It indicates that projects like ALCHEMIST, which will put discoveries about molecular alterations to the test in a clinical setting, will improve our understanding of the molecular mechanisms of tumor resistance and our ability to treat cancer based on the characteristics of an individual’s tumor. With a new chapter in cancer genomics that links clinical and molecular data, the cancer research community will be better situated to apply cancer genomics to clinical care.