Center profile: UC Davis Genome Center

Pioneering technology at the forefront of genomics research

12/05/12

The UC Davis Genome Center is a data hub like no other. Housing the most cutting-edge genomics sequencers and mass spectrometers in the world, the center provides enabling technological services to any researcher in need of fast, at-cost support for a project.

By doing so with the expertise of its faculty—all top-notch, technology-driven biologists—it produces world-class research both by itself and by supporting the campus’ diverse scientific departments.

The center’s five service cores offer expert support in the areas of DNA sequencing, expression analysis, metabolomics, proteomics and bioinformatics.

“We want the faculty to think of our service cores as being an extension of their own labs,” founding director Richard Michelmore says. “We can guarantee that the machines will be state-of-the-art and the technicians will be the best in the world.”

And although the center makes services available to outside researchers and commercial entities when not fully booked by UC Davis faculty, campus scientists always receive priority.

“We are the genomics technology antenna for campus and are here to provide intellectual and technical support. If anyone on campus has a bright idea, they shouldn’t be technologically limited,” he says.

The idea of centralizing these services on campus arose in the 1990s, when a revolution in biology was being driven by many technical advances from the early human genome project.

“Biology was becoming more computational and the genomic components of biological and medical studies were becoming more essential,” Michelmore says. “The center was established as a way for UC Davis to respond to those rapid changes and keep current.”

In addition to acquiring the latest in genomic, proteomic and metabolomic instruments, the genome center provides an interdisciplinary environment for researchers to discover commonalities between organisms from plants to humans.

“With the new technologies, the basic paradigm of life is increasingly being worked out in model species. The strength of our campus is that we study so many different organisms here. So what we need to do is to investigate how the basic paradigms play out across biology,” Michelmore says.

“It’s comparative functional genomics. And there’s nowhere like Davis in the world that has the diversity and strengths that we do – that’s why it’s essential we’re at the cutting-edge of biology.”

Professor Savithramma Dinesh-Kumar, a plant biologist who joined the faculty three years ago, says this diversity attracted him to campus. “We are organized in a way that is interdisciplinary, which is the main reason I came here, because my lab is interested in cutting-edge proteomics,” he says.

Dinesh-Kumar’s lab studies how plants respond to pathogen infections. Collaborating with Genome Center Associate Director David Segal, he has recently been awarded a challenge grant from the Gates Foundation to seek a way to develop a virus-resistant form of cassava, an important African food crop.

“My group is very much interested in proteomics technology and at UCD Genome Center we have cutting-edge mass specs that aid in our proteomics work,” Dinesh-Kumar says. “The sensitivity is at least five times higher than previous equipment and we can identify proteins that were not possible in the past.”

The Dinesh-Kumar lab at the center has also established a “protein chip” platform to analyze thousands of proteins simultaneously for in vitro biochemical activities in a high throughput manner.

In addition to acquiring the latest technology to enable the best research, the center has made a name for itself as a go-to beta tester for new sequencers and other equipment.

“One of our other roles is to act as an interface between developing technologies and the scientific community,” Michelmore says, adding that beta-testing puts Davis really on the bleeding edge of advancements, providing faculty with the newest technologies possible.

“Because we have the reputation that we do, if we validate a new technology for the company, we give them credibility,” he says. “It’s a win-win-win—for us, the company and scientific community.”

On a tour of the center, Michelmore shows off one of their newer machines, Illumina’s Hi-Seq DNA sequencer. It can sequence as much data in four days as had been collected by the GenBank up to 2009.

Another example is the center’s PacBio DNA sequencer. There are only about 60 of these in the world and its specialty is sequencing very long molecules.

This allowed Professor Paul Hagerman to measure the repeat length in the gene causing fragile X syndrome, associated with neurodevelopmental disorders and the most commonly known single-gene cause of autism.

“The thing about fragile X is it’s unstable and even within an individual it can vary. Fragile X is very difficult to read with other sequencing technologies, but the PacBio sails through it,” Michelmore says. “Because we have one at the center, we were able to provide this niche application to a UC Davis researcher.”

Such “toys,” as the machines are affectionately called, also help recruit high-caliber faculty to campus.

“There is a subset of researchers who love technology and can’t put it down,” Michelmore says. “These are top-class scientists but are often faculty members who are not necessarily fully appreciated in a hypothesis-driven environment. We provide a home for technology-driven biologists and they are very happy here.”

Plant biologist Siobhan Brady—recently named a top young investigator by Genome Technology Magazine—would be appreciated in any environment. Brady received multiple offers from other universities when applying for tenure-track positions a few years ago, but Davis’ reputation for its premier plant-bio program drew her here.

“And the opportunity to be part of the Genome Center was the deal breaker,” says Brady. “I had the opportunity to work with faculty in diverse research areas who all incorporate genomics and many of whom are the leaders in terms of successfully using new technology and developing methods to analyze large-scale genome data.”

In addition to pursuing top research and being very collaborative by nature, a common expectation of genome center scientists is that they keep their eye out for the next best technology in their specialty.

“This place is a great mix of scientists who are heavily encouraged to go out and use new technology and incorporate it in their programs, as well as to develop novel training programs and courses. In other institutions you rarely have that mix of biologists with adopters of new technology across such a diverse set of fields,” Brady says.

According to Brady—who last year published a novel high-throughput yeast one hybrid screening methodology for use in plants with the help of something called a “yeast pinning robot”—the center is fulfilling its mission with flying colors.

“At each Genome Center faculty meeting I come out feeling so excited about the research that is going on here and I always have a feeling that I am on the cutting edge,” she says.

The center also seeks to provide intellectual leadership in genomics to the campus, for example in its participation in two interdisciplinary planning groups: the Big Data Initiative, which is focused on how to keep current in a data-rich scientific environment and the Human Genetics and Genomics Initiative, which has the mission of strengthening UCD’s research in human genetics.

“Human genetics is about to change society as much as the computer has. Society is woefully unprepared for it and the campus also needs to prepare for this,” Michelmore says.

"We have tremendous strengths in areas such as chromosome biology, evolution and ecology, nutrition, and in the Medical School such as the Cancer Center and the MIND Institute as well as the Vet School. We need to bring all these assets together and recruit more human geneticists to create something world-class."