The CTD2 Dashboard: A Platform to Explore Evidence-based Observations
March 2, 2016, by Amy E Blum, M.A.
The Cancer Genome Atlas (TCGA), TARGET, and other large-scale sequencing projects such as the International Cancer Genome Consortium (ICGC), have catalogued a vast number of genetic abnormalities in cancer. However, identifying these abnormalities is just one part of the puzzle.
Next, cancer researchers need to determine which changes drive cancer development, metastasis, and drug resistance, and how this information can be used to improve cancer care and early detection. To help researchers translate genomics into therapies, The Cancer Target Discovery and Development (CTD2) Network functionally validates genomic research and displays the resulting evidence-based conclusions on the CTD2 Dashboard, an interactive web interface for exploring cancer biology.
Connecting Genomic Discoveries to Cancer Biology
As described by Dr. Louis Staudt, MD, Ph.D., in his piece, Divide and Conquer: The Molecular Diagnosis of Cancer, understanding how to utilize the “parts list” of genomic changes toward precision oncology can be done either through computational genomics, which uses advanced computational tools like algorithms to decode the meaning of genetic changes in silico, or it can be done in the lab, through functional genomics.
CTD2 is a CCG program that uses both computational and functional genomics to bridge the gap between the enormous volumes of data generated by genomic characterization and the translation of these findings. Thirteen Centers across the United States mine data from the “parts list” of cancer genomic alterations, perform functional tests of key genes, and identify approaches for detecting and targeting these changes. Then, their findings are assembled into a user-friendly web interface for cancer researchers to browse, discover, and make new connections.
The CTD2 Dashboard
The CTD2 Dashboard makes discovering connections between genes, proteins, perturbagens, and diseases simple for users across the spectrum of cancer research, from cancer biologists to interested students. Research findings, or observations, generated by CTD2 are put onto the dashboard and tagged by the subject of the research. These tags facilitate exploration of important biological connections by linking to background information and other relevant observations.
The interconnected CTD2 observations are then classified into Evidence Tiers to help users visualize the flow of research from laboratory investigation in vitro to biological validation in vivo. The tiers are based on the strength of the supporting data, as follows:
- Tier 1 is composed of preliminary observations.
- Tier 2 is assigned to results with confirmation in vitro.
- Tier 3 indicates that experimental results have been validated in a cancer model in vivo.
Ranking the biological evidence for each observation into tiers helps to define which observations are robust enough to use in the development of cancer biomarkers and targeted therapies, and which deserve further investigation.
To ensure that users have a complete understanding of observations, the CTD2 Dashboard also provides detailed summaries of CTD2 publications that include important scientific context, descriptions of the methodology employed, the study’s results and interpretation, and resources to learn more.
CTD2 is a community resource project that releases its raw and analyzed primary data onto the CTD2 Data Portal and its subsequent conclusions onto the CTD2 Dashboard for unrestricted, open access. As CTD2 centers continue to make critical connections between cancer genes and their functional role in cancer, the dashboard will incorporate these observations into its growing network of evidence, and become an even greater resource for the scientific community. To learn more about the CTD2 Dashboard and its functions, visit the Office of Cancer Genomics CTD2 Program Highlight.