The Tasmanian Devil 2: The tumor and Tasmanian devil mitochondrial genomes

The Tasmanian devil (Sarcophilus harrisii), the last remaining large marsupial carnivore, now faces extinction because of a strange and deadly infection, a transmissible cancer known as Transmissible Devil Facial Tumor Disease (TDFTD).  In a previous NCBI Insights post, we discussed gene expression data from the tumors that established their neural origin and showed the tumors were likely derived from Schwann cells.  In this post, we’ll consider some of the genome sequencing projects in the NCBI databases and explore evidence that the tumor originated in a different individual than the affected animal supporting the idea that the tumor cells themselves are infectious agents. Continue reading

NCBI’s Open Data – A Source of Experimental Data for Important Discoveries

On a typical day, researchers download about 30 terabytes of data from NCBI in an effort to make discoveries. NCBI began providing online access to data in the early 1990s, starting with the GenBank database of DNA sequences. Over the years we’ve greatly expanded the types and quantity of data available. You can now find on our site descriptions and data from experimental studies such as next-generation sequencing projects, bioactivity assays for small molecules, microarray datasets and genome-wide association studies.

The White House recently recognized these efforts by awarding NCBI Director David J. Lipman with the “Open Science” Champion of Change Award [1]. The scientific community has recognized the benefits of open data. Access to this information serves as  a source of both original and supplemental data for exploration and validation [2-4], which improves the power of experimental data [5] while increasing the speed and decreasing the cost of discovery [6].

In this post, we summarize three recent cases where researchers used data from an NCBI resource/database to make significant discoveries.

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The Tasmanian Devil and Cancer as an Infectious Disease: Analysis of transcriptome data

The Tasmanian devil (Sarcophilus harrisii), the last remaining large marsupial carnivore, now faces extinction because of a strange and deadly infection: a transmissible cancer known as Devil Facial Tumor Disease.  These tumor infections are apparently passed to other devils through bites during mating or during squabbles over carrion when devils gather to feed. In this unusual situation, the cancer cells themselves are the infectious agent.

The failure of devil immune systems to recognize and destroy the foreign tumor cells may be related to a decline in genetic diversity and may serve as a warning about the vulnerability of species with reduced gene pools.  The advent of next-generation sequencing has provided an unprecedented opportunity to track the spread and identify the origin of this unusual zoonosis, as well as to examine the population structure of an endangered mammal and generate a complete genome sequence for this unique marsupial.

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