VCU news

By Anne Buckley

The Center for the Study of Biological Complexity at Virginia Commonwealth University has augmented its high throughput genomics capabilities with the acquisition of two pieces of equipment that reduce the amount of time it takes to sequence a genome from years to weeks, and in some cases, days.

The sequencing capabilities, combined with the ongoing genomics research in VCU's biomedical research laboratories and the recent recruitment of two high-profile genomic scientists from Harvard University and the University of California at Los Angeles, are in step with VCU's strategic priority to achieve continued recognition as a top research institution.

The 454 GS FLX instrument from Roche provides more than 100 million bases of sequence in an eight-hour run, a greater than 100-fold improvement over existing technology. The Solexa 1G Genetic Analyzer will provide more than a billion bases of sequence per run, a 1,000-fold enhancement over current technology.

The combination of the equipment will reduce the cost of genome sequencing to a fraction of the cost of previous sequencing projects, said Gregory A. Buck, Ph.D., director of the CSBC in VCU Life Sciences.

"We spent four years and more than $2 million on our recent sequence of the 10-megabase Cryptosporidium hominis genome," Buck said. "With the new instrumentation, we could reproduce that effort in two weeks for a cost well south of $100,000."

C. hominis is an important intestinal parasite and a CDC-rated potential agent of biological terrorism. Buck's sequencing team, together with the lab of Francis L. Macrina, Ph.D.; VCU's vice president for research, also recently published the sequence of Streptococcus sanguinis, an oral pathogen and major cause of bacterial endocarditis.

"With the new technology, we could have finished that sequence in a single day," Buck said.

In addition to Buck and Macrina, an interdisciplinary group of researchers at VCU plans to use the sequencer for projects ranging from metagenomic analysis of environmental samples to resequencing human chromosomes to identify genes associated with complex human diseases.

Macrina said VCU is poised to make great strides in the field.

"VCU has been a leader in genomic research," he said. "The $1,000 genome and personalized medicine are just around the corner, and VCU will be there when it happens." The $1,000 genome is the new "holy grail" for genomic scientists since the X PRIZE Foundation announced a $10 million cash prize for the first privately financed team to accurately sequence the human genome for less than $1,000 in fewer than 10 days.

VCU's push toward pre-eminence in genomic research also includes the recruitment of Yuan Gao, Ph.D., from Harvard, where he had been working with George Church on 2^nd generation sequencing technologies, and Maria C. Rivera, Ph.D., from UCLA, where she worked with noted evolutionary biologist James Lake. Rivera's groundbreaking work focuses on applying comparative genomics leading to the proposal of a "Ring of Life" as an alternative to the traditional "Tree of Life."

Gao's wet lab will host the Solexa machine and use it for high throughput genome sequencing, gene expression profiling and Personal Genome Project, in collaboration with Church's lab at Harvard.  Rivera will use the technology to confirm and extend her controversial new theory on the origin of eukaryotes. Their work reflects the multidisciplinary aspect of Life Sciences, as they also have appointments in the VCU School of Engineering and its College of Humanities and Sciences.

"VCU Life Sciences is all about systems biology," said Thomas F. Huff, Ph.D., vice provost for VCU Life Sciences, the home of the Center for the Study of Biological Complexity. "High throughput sequencing is the breakthrough technology that led molecular and cellular biologists into systems biology."

The Center for the Study of Biological Complexity is a matrix academic unit of VCU Life Sciences. The Center focuses on integrative discovery science, systems biology, and the principles of complexity to address the challenges of the life sciences revolution of the 21st century. Nearly 100 VCU faculty members in more than a dozen departments and five schools and colleges are fellows. The CSBC maintains research infrastructure for the support of genomics, transcriptomics, and proteomics, and houses VCU's high performance computing and bioinformatics facilities.