The Cancer Molecular Analysis Portal launches with GBM data from The Cancer Genome Atlas Network
With more than 1,400,000 cancer diagnoses in the United States in 2007, the need to diagnose, treat, understand, and prevent cancer is greater than ever. Innovative biomedical technologies are helping researchers to learn more about the molecular basis of cancer at a faster rate than ever before, and researchers are now faced with the challenge of working with massive, often disparate data sets to drive innovation. This summer the National Cancer Institute (NCI) unveiled the Cancer Molecular Analysis (CMA) portal, a new online resource that enables collaboration between the broad scientific and medical communities to accelerate discoveries.
The CMA portal provides online access to large, disparate data sets and to the tools required to analyze the data. A single interface allows researchers to integrate, visualize, and explore clinical and genomic characterization data from translational research studies.
“In this era of molecular medicine there is great potential to connect scientific discovery, clinical research, and clinical care into a seamless continuum,” said Dr. Ken Buetow, associate director for Bioinformatics and Information Technology at the National Cancer Institute (NCI). “The CMA portal is a leading example of a collaborative, open-development resource that is expected to save researchers time and energy.”
Brain Cancer Data from The Cancer Genome Atlas
The first data set available on the CMA portal was generated by The Cancer Genome Atlas (TCGA) Pilot Project, a coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. The TCGA Research Network pulled together and integrated multiple types of data generated by investigators at more than 18 different participating institutions and organizations.
On September 4, 2008, in the advance online edition of Nature, TCGA reported the first results of its large-scale, comprehensive study of the most common form of brain cancer, glioblastoma (GBM). Among the TCGA findings are the identification of many gene mutations involved in GBM, including three previously unrecognized mutations that occur with significant frequency; and the delineation of core pathways disrupted in this type of brain cancer. Among the most exciting results is an unexpected observation that points to a potential mechanism of resistance to a common chemotherapy drug, temozolomide, used to treat glioblastoma patients.
Through the CMA portal, users can gain access to the same data sets used to generate such discoveries. The CMA portal integrates the large-scale data collection of TCGA with unprecedented integrative power to allow for a multi-dimensional network view of gene pathways and common genetic changes in the GBM genome. The recent GBM findings provide an initial indication of the many advantages on the horizon as users integrate more and more large-scale data sets.
“This is truly a turning point and exciting time for TCGA,” stated Dr. Daniela Gerhard, director for the Office of Cancer Genomics at NCI. “As we gain valuable insights into the biology of GBM and identify new potential targets for cancer intervention, CMA provides analysis tools that will enable us to gain more insights into the mechanisms of cancer.”
The Crossroads of Cancer Data
The value of the CMA portal will grow as additional data sets for various types of cancer are added over the next few months. Future additions include lung and ovarian cancer data sets from the TCGA pilot, brain cancer data from the REMBRANDT study, and childhood cancer data from the TARGET Initiative.
“The CMA portal is a unique resource because it has the ability to integrate, and even compare disparate databases,” explained Dr. Subha Madhavan, former associate director of life sciences informatics at the NCI Center for Biomedical Informatics and Information Technology. “Users will have the ability to dig through the data and find what is most valuable to their particular study.”
As additional data sets become available for integration to the portal, CMA developers will need to address the challenges of data sharing and security issues.
“Data sharing and security plays an essential role in the CMA portal,” said Madhavan. “We are currently addressing these issues through a tiered system of access, moving from the first tier of open-access to a controlled-access tier that requires user certification.”
Focus on the User
One of the goals of the CMA portal is to provide an easily accessible user interface. In a presentation at the 2008 caBIG® Annual Meeting, Mark Adams, senior associate at Booz Allen Hamilton, explained how, through the CMA portal, users can carry out a range of high-level analyses and make use of existing workflows that integrate a variety of informatics tools and outside data resources. “These workflows can be stored, recalled and potentially shared with colleagues.”
The CMA provides researchers with four ways to view data:
- Gene View allows users to visualize gene expression, copy number, SNP, and pathway data on a gene-by-gene basis and to generate detailed study-related reports for a given gene.
- Genome View allows users to investigate chromosomal regions of amplification, deletion, and over-expression, and zoom in a chromosomal region of interest, all in one genome-level visualization.
- Clinical View allows users to explore the relationships between clinical and molecular study data.
- Analysis Tools help users analyze the gene expression data from the study using analysis tools such as Genepattern, Principal Component Analysis, and the Cancer Genome Workbench.
Learn more
Click here to access the Cancer Molecular Analysis portal.
Click here for more information on The Cancer Genome Atlas Data Portal.
Click here to learn more about The Cancer Genome Atlas Pilot Project.
