St. Louis-area scientists now have easy local access to sophisticated technology to decode and analyze the genomes of patients and organisms in research studies.
The Department of Genetics at Washington University School of Medicine in St. Louis has established the Genome Technology Access Center (GTAC) to offer high-speed genome sequencing and other advanced genetic technologies to scientists both within and beyond the university.
In recent years, genomics has revolutionized the field of biology, enabling researchers to investigate the spectrum of genetic mutations that underlie human diseases as well as host-pathogen interactions, genome evolution, microbial ecology and other biological matters. Genome sequencing involves spelling out the precise order of chemical bases, represented by the letters G, A, T and C, in a molecule of DNA. Such a task used to take years but can now be accomplished in a few weeks’ time.
But the technology has remained out of reach for many laboratories. That’s because DNA sequencing machines cost hundreds of thousands of dollars, making them unaffordable for individual labs. Moreover, many scientists don’t have the expertise to analyze the terabytes of genomic data produced by sequencing.
“DNA sequencing has become the go-to technology in many fields,” says Jeffrey Milbrandt, MD, PhD, the James S. McDonnell Professor of Genetics and head of the genetics department. “But not every scientist has the specialized training to prepare DNA samples, analyze the data and interpret the results. We saw a real need to fill these gaps and to expand access to the technology.”
Rob Mitra, PhD, associate professor of genetics, has been a driving force behind the new center.
“Rob’s broad-based expertise in genetics and genomics has been invaluable to the development of GTAC,” Milbrandt says. “He has assembled a first-class team.”
The center is staffed by nearly 20 scientists, including geneticists, molecular biologists and informatics specialists, who have the expertise to prepare DNA samples for sequencing and to analyze and interpret the data.
“We can make biological sense out of the massive amounts of sequence data and put it in a format that scientists can understand – that’s a real strength of ours,” Mitra says.
GTAC is distinct from Washington University’s Genome Institute, which has been in existence for nearly two decades and is one of three sequencing centers funded by the National Institutes of Health (NIH) to carry out very large-scale projects. The new center can handle both small and large projects, and its services are offered to scientists on a fee-for-service basis.
GTAC already has begun to provide genome sequencing and analysis to Washington University researchers and to local scientists at Pfizer, Sigma-Aldrich, Nestle, Saint Louis University and at the Stowers Institute for Medical Research in Kansas City.
“The center is an economic boost to the entire region,” Milbrandt says. “In addition to hiring scientists to do sequencing and data analysis, we are keeping dollars in St. Louis that almost certainly would have been spent elsewhere.”
GTAC has five of the latest Illumina DNA sequencing machines and another is on order. The machines are located on the School of Medicine campus and in the Center of Research, Technology & Entrepreneurial Exchange (CORTEX) building, just east of the Medical Center. The CORTEX location is convenient to a number of biotech companies and startups.
Researchers who have DNA to be sequenced can opt for whole-genome sequencing, which spells out the entire sequence of chemical bases that make up DNA; exome sequencing, which looks only at the sequence of bases in protein-coding genes; or other methods, including those that examine RNA, selected regions of the genome, or chromatin. In addition, other DNA and RNA characterization technologies such as microarray and quantitative PCR are available.
“We have the full range of technologies needed to perform genetic analyses,” says Seth Crosby, MD, center director and research assistant professor of genetics. “Scientists don’t have to know the details of a particular technology. We can walk them through the various options and help them select the best one based on the research questions they want to answer.”
The entire process – prepping DNA samples, sequencing and analysis – can take as little as two weeks, depending on the type of sequencing and the number of samples. To enhance the ability to analyze massive amounts of genetic data, a number of informatics pipelines has been established under the leadership of Paul Cliften, PhD, director of computational biology at GTAC and research associate professor of genetics.
Scientists also can choose to prepare their own DNA samples or analyze the raw genomic data if they prefer. For help with the analysis, investigators also have access to the Center for Biomedical Informatics, directed by Rakesh Nagarajan, MD, PhD, associate professor of pathology and immunology, and Washington University’s high-performance computing facility, directed by Fred Prior, PhD, research associate professor of radiology.
For more information about the Genome Technology Access Center, please visit the website, http://gtac.wustl.edu, or call Crosby at 314-286-1256.
Washington University School of Medicine’s 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children’s hospitals. The School of Medicine is one of the leading medical research, teaching and patient care institutions in the nation, currently ranked fourth in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children’s hospitals, the School of Medicine is linked to BJC HealthCare.