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Rachel Cherney
At Oncobites, we write about current and cutting edge cancer research and how various lifestyles may affect cancer risk. However, we don’t often talk about the types of data that are generated from cancer research or how they can be used. Large informative data sets can be used to look at multiple aspects of cancer. However, most data aren’t used in that way, which results in an underused reservoir of knowledge.
To attack this problem, the National Cancer Institute and the National Human Genome Research Institute created The Cancer Genome Atlas (TCGA), a project to compile cancer research data into one location. TCGA compiled data for 33 different cancers (out of over 200 types of cancer). These 33 cancers were chosen for study based on the ease of collecting patient samples, cancer impacts on public health, and the overall poor patient survival rate. Altogether, TCGA has compiled data from over 1000 studies and over 10,000 patient samples. The datasets can be found at the Genomic Data Commons (GDC) and are publicly available to scientists around the world. Further study and analysis of cancer characteristics will ultimately lead to better and more effective cancer treatments. A paper overviewing TCGA and its results is publicly available and can be found here. In a free on-demand webinar, four contributors of TCGA talk about the most intriguing results from their project.
The Cancer Genome Atlas data compilation ended in April 2018, and evolved into the Pan-Cancer Atlas, with the goal of “understanding how, where, and why tumors arise.” The Pan-Cancer Atlas serves as a hub of scientific papers which used TCGA data to analyze cancers in a multitude of ways, including better understanding how certain cells become certain cancers, the communication pathways inside cells that break down, and how the body’s immune system reacts to different cancers.
Cancers are caused by mutations in the DNA that result in cells that do not work properly. Mutations can include translocations, which is when two different chromosomes break apart and then fuse together to become a new chromosome. This combines parts of genes that otherwise would not be present in normal cells.
The photo above shows many colorful lines that join two chromosomes and describes cancer or disease associated with the translocation. Translocations and segregation of chromosomes during cell division can result in aneuploidy, which is when an individual has an irregular number of chromosomes or chromosome parts. In this Pan-Cancer Atlas paper, the authors were able to use TCGA data to observe that certain types of cancer were more likely to have cells with translocations and aneuploidy. A group of gastrointestinal cancers (stomach and intestinal cancers) was found to be enriched in aneuploidy with an increase in parts of Chromosome 13 and loss of parts of Chromosome 18. So if a patient has a Chromosome 13/18 translocation, they are more likely to develop gastrointestinal cancer.
With extensive analysis of the data provided by TCGA, scientists and physicians may someday have an actual road map of cancer. Starting from which cell cancer began in, we could one day follow the directions genetic mutations provided us to create effective treatments to reach our final destination: cancer elimination.
Work Discussed:
Hoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., . . . Laird, P. W. (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173(2), 291-304 e296. doi: 10.1016/j.cell.2018.03.022
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