Richard Casey and Erin Petrilli are pretty stoked to share their latest data with the National Wildlife Research Center. The NWRC is concerned about the Florida Everglades and its rapidly growing population of unwanted pythons – non-indigenous snakes with no natural predators and a rich prey base. The pythons are reproducing as fast as Internet memes and swallowing everything in their path, decimating native wildlife populations. But the snakes also can be difficult to track down, undermining the NWRC’s efforts to determine their true population size, current territory, and expansion patterns, and develop effective control measures.
To better understand these unknowns, the NWRC turned to the Colorado State University’s Next Generation Sequencing Core located at the Research Innovation Center on CSU’s Foothills Research Campus. Whole genomic sequencing, using the Ion Proton and Ion Torrent systems from Life Technologies, means NWRC can search for snakes in a whole new way.
“Using this technology, we can take NWRC water samples from the Florida Everglades and pretty much see the DNA of almost every species living in that area of water,” said Casey, the bioinformatics specialist at the lab. “If python DNA is in the water, pythons are in the area. We’re just finishing up our first samples, and I think the NWRC will be pretty astounded by what’s hanging out in the Everglades.”
The new semiconductor-based sequencers use an approximately 1-inch-square computer chip with 160 million wells on the top side. Microscopic samples such as water, blood or soil are injected into the chip and spun into the wells using a centrifuge. From there, the chips are inserted into the sequencer; the Ion Torrent for smaller biological organisms including bacteria and viruses, and the Ion Proton for larger organisms. Working with the sequencers is the university’s Cray Supercomputer. In the case of the NWRC samples, the supercomputer looks at a database of 15 million DNA snippets to match the genomes in the Florida Everglades’ samples and assess which species are present. New chips due out this summer will have 660 million wells, increasing the numbers of samples that can be placed on one chip. In 2014, the new P3 chip will have 1.2 billion wells capable of running two-to-three whole human genomes on the same chip.
Colorado State University is one of the few places in the world with the revolutionary semiconductor sequencing technologies and computing power needed to put this type of data into the hands of NWRC researchers. But searching for python DNA is just the tip of the genomic iceberg. In fact, in July, the laboratory will be offering complete sequencing of the human genome – fast and at an affordable price (not available for those just curious about the diseases lurking in their DNA).
The laboratory currently has projects with the Mycobacteria Research Laboratories sequencing the tuberculosis bacterium, particularly looking at genetic changes brought about by exposure to different pharmaceuticals. In another study, soil samples from area feedlots are under investigation for the presence of listeria, searching for patterns of when the bacteria is present and when it is not, and looking at the bacteria’s genome. The possibilities for the types of research that can be positively impacted by the technology are almost endless, said Petrilli, who is the laboratory manager and takes care of the front-end details of the Next Gen genomic studies including sample preparation.
“For the research community, this new technology is a complete game changer,” said Casey, who provides expertise in bioinformatics, analytics, software, and databases. “The cost is inexpensive, especially when compared to older technologies; the turnaround time is fast, several hours compared to several weeks; and the dataset is rich.”
Next generation sequencing gives tremendous potential for new discovery and is setting a new standard in genomic-based investigations. It enables massively parallel sequencing of nucleic acid fragments to address a variety of experimental questions including DNA sequencing and whole transcriptome analysis. With such a wealth of data, investigators work closely with the Next Generation Sequencing team who help design the project, and develop robust bioinformatics to get the data the investigators want. Close collaboration with Casey and Petrilli are an important part of these collaborative studies and can help improve grant applications.
Plus, python hunting in 50 micrograms of swamp water is a heck of a lot safer than tracking the really big snakes in the swamps of Florida.
The CSU Next Generation Sequencing Core in the Infectious Disease Research Center offers services in experimental design, sample preparation, DNA sequencing, bioinformatics and data analysis, computational resources, and data management.