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Applied Biosystems and Dr. William Farmerie

A partnership for the advancement of science

William G. Farmerie, Ph.D.
Associate Director

Interdisciplinary Center for Biotechnology Research
University of Florida

Founded in 1988 by the Florida state legislature, the Interdisciplinary Center for Biotechnology Research (ICBR) is a research support organization, which provides high-end technical services to the research community at the University of Florida, as well as across the State of Florida and beyond.

We recently had the opportunity to talk with Dr. Bill Farmerie, ICBR's Associate Director, about how the Center is using the Applied Biosystems® SOLiD™ System to help researchers find new ways to ask questions and interpret data.

Tell us a little about the purpose of the ICBR.

The ICBR was founded around 1988 as a research-support organization. It consists of four major divisions—Cellomics, Proteomics, Bioinformatics, and Genomics—whose research support laboratories provide more than 250 technical services as diverse as electron microscopy, flow cytometry, mass spectrometry, genetic analysis, and next generation high-throughput DNA sequencing. University of Florida (UF) has a very diverse scientific community spanning from medicine to agriculture. If you were going to set up a DNA sequencing operation, you would really have a hard time picking a better place than the University of Florida to do it.

What areas of research is the ICBR engaged in?

We have a medical school, a dental school, a college of pharmacy, and a school of veterinary medicine, which means we have research scientists working in many areas relevant to human and animal health. We are also home to the Florida Museum of Natural History, and UF is also Florida's land grant institution. Hence, we have a very large agricultural presence both on campus and in a network of laboratories located throughout the state.

Our laboratories also do work for the biotechnology industry in the state of Florida and for other universities around the country and around the world. Many scientists want to collaborate with UF faculty in order to gain access to the expertise ICBR brings and the leading-edge technology we provide here. So the short answer is, we are involved in pretty much everything—from medically based research to crop science, animal science, and veterinary science. It's really a very fertile place to be to be doing this kind of work.

How important is next-generation sequencing to the ICBR and the research you conduct here?

We made the decision to adopt next-generation sequencing very early on, when the first instruments were just arriving on the market. Right away, it had a tremendous impact on productivity and cost efficiency, and essentially transformed how we thought about doing life sciences research. After a couple of years, new short-read instruments that had a completely different impact from the original instruments became available, and allowed us to expand the scope of projects we could do for our clients.

Today, next-generation sequencing is critically important to ICBR because it is a broadly enabling technology with critical importance to the research community. Our role in the university is to identify transformative technologies and make them available. The way our research community has embraced it is actually quite amazing as well as gratifying.

What are the major considerations the Center has to weigh when adopting a new technology like a next-generation sequencing system?

As a service facility, it is just as important to be able to add value to raw data after it streams out of the machine, as it is to acquire the data in the first place. So, when we're planning for the future, one of the things we spend the most time thinking about is how we're going to stay ahead of the curve and how we're going to keep up with increasing demands placed on information management and data analysis systems. Because once you put a technology in the hands of the research community, they immediately begin to find new ways to use it.

Each next-gen application, and there is an ever expanding range of applications, has its own set of computational requirements for interpreting the raw data. It's computation that gives raw sequence data its meaning, and if we can't handle the volume of data we generate with these instruments, then we're done. We're toast. That's what it's all about—the research world will be divided into those who can do the computational work and those who can't. So that's one of the things we press here: "Do we want to be able to do sequencing and computation or do we want to sit back and watch everyone else do it?"

Why did you choose the Applied Biosystems SOLiD™ system over other next generation sequencing systems?

We were comfortable with the idea of next generation sequencing through our experience with an earlier platform, but it was becoming clearer there was an entirely new sphere of applications for instruments that produced hundreds of millions of short sequence tags. We started a dialog with Applied Biosystems not long after they acquired SOLiD™ technology, and I was immediately intrigued by the notion of two base encoding. I felt single nucleotide polymorphism (SNP) hunting was certainly one of the applications we would use this for, and the accuracy of the SOLiD™ System was very appealing.

Furthermore, Applied Biosystems is just technically superb. They know what they're doing and they have a great reputation for keeping their promises when it comes to bringing new technology to the research community—that's essential in a remarkably fast-moving field like DNA sequencing. I was also impressed with their very workable strategy for doing mate-pair sequencing, which I thought was going to be a really big feature—and I was right!

How would you describe your collaborative relationship with the SOLiD™ Sequencing team at Applied Biosystems?

Applied Biosystems has been wonderfully supportive. As one of the early adopters of the technology, we had constant contact with the SOLiD™ System technical staff for training, troubleshooting, and generally working our way through the process. The high level of customer service was key, because the technology was so new that we couldn't anticipate all the issues that might arise. But, whenever we asked them a question, they came right back with an answer. They helped us get up to speed quickly to where we could use the instrument the way it's intended to be used and start pushing the applications envelope into the future.

Can you give us some examples of the kind of projects you're doing on the SOLiD™ System here at the ICBR?

One of the first things we were approached about doing is a technique called ChIP-Seq, which is used among other applications, for looking at specific protein interactions in chromatin in order to identify regions of the genome that are being expressed. We also worked on bacterial genome resequencing, which involved looking at serial isolates of a bacterial species having variant phenotypes.

Recently, we've been doing a lot of human genome resequencing using mate-pair libraries, because the cancer research community is intensely interested in looking at genomic rearrangements in various kinds of cancers. We have some exciting new possibilities for our work with Moffitt Cancer Center in Tampa, as well as our own cancer center, that are driven by the new applications for SOLiD™ Sequencing.

There's also huge buzz right now about RNA—Seq, and I think that will be the focus of the next set of projects for the SOLiD™ System.

What excites you most about the work you're doing at the ICBR?

Our role in the research process is to provide individual investigators with the technology, the technical expertise, and the computational infrastructure required to produce and interpret raw DNA sequence data. They can come to us with an idea and we help find ways to apply technology to the question at hand. It's very satisfying to enable technology that helps scientists arrive at that "Eureka" moment, where they make a discovery or solve a mystery they've spent a part of their career working on.

That's what makes this business so darn exciting — it is constantly evolving and you just have to ride the wave, because there is always something bigger, faster, and cheaper just over the horizon. What we can do today is just scratching the surface of what we will be doing tomorrow or next week or next year—that's how fast these instruments are advancing. I love being able to bring new capabilities to the research community and participate in so many different kinds of projects. I can't imagine doing something more exciting than playing this particular role.

What direction do you see your future work with the SOLiD™ System taking?

The research community is prospecting for funding to do some pretty exciting projects. There's no question that the possibilities for medical resequencing are pretty much limitless, and there is tremendous interest in the instrument from the medical community, especially cancer researchers. We're also seeing a lot more happening on the agricultural side especially as additional genome sequences emerge, so I'm confident that we are going to be using this technology across the board.

I also think a major new area of research will center on exploring the intricacies of the transcriptome. We really don't appreciate the full extent of the diversity of transcribed molecules. But, with the SOLiD™ System, we have the technology to probe gene expression at a completely new level.

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