Speed of genome sequencing gets big boost from small package

For technicians in the Genome Sequencing Center (GSC) at Washington University School of Medicine in St. Louis, work is going to go a whole lot faster — hundreds of times faster, in fact. Fast enough to sequence the entire genome of a bacterial organism in one day instead of several weeks.

That’s because the GSC has acquired a next-generation DNA sequencer to determine the order of a genome’s DNA units, or bases. No other DNA sequencer has its capacity and ease of use.

The entire machine is only about the size of a suitcase, whereas the current capillary-based sequencers used in the GSC are the size of a refrigerator. The installation of the new sequencer at the GSC is only the second installation of this new instrument anywhere in the world.

“This platform churns out sequence data far faster than our capillary-based sequencers,” says Elaine R. Mardis, Ph.D., co-director of the GSC and assistant professor of genetics and of molecular microbiology. “Here hundreds of thousands of sequencing reactions happen at once, and the instrument reads them all simultaneously. It’s a massively parallel approach to DNA sequencing.”

The whole-genome approach utilized by this instrument also eliminates a lot of preliminary laboratory work required by other sequencing equipment. Researchers need only perform one sample preparation per genome and don’t have to go through steps to amplify the DNA in bacterial systems.

“It’s not only efficient, it’s very cost-effective,” says Richard K. Wilson, Ph.D., director of the GSC and professor of genetics and of molecular microbiology. “Our older sequencers cost about $350,000 and handle about 2,000 samples per day. The new machine costs $500,000, but it can run through 800,000 samples in an eight-hour workday.”

The GSC receives funding from the National Human Genome Research Institute at the National Institutes of Health. It has been a vital part of Human Genome Project, the international research effort that sequenced the entire human genome. GSC researchers were primarily responsible for sequencing chromosomes 2, 4, 7 and Y, producing the initial analyses of more than 20 percent of the human genome.

“This is the first new technology for large-scale DNA sequencing that has been developed and introduced in the 15 years that we’ve been doing genome sequencing at Washington University,” Wilson says. “It has spurred a lot of ideas about what the GSC can accomplish with it.”

With the reference sequence of the human genome complete, the new instrument will be useful for quickly resequencing additional human genomes to find variations that can provide insight into disease states. For example, comparing the reference sequence to the sequence of genes in cancerous cells can pinpoint genetic variations that may be responsible for initiating cancerous growth.

“Because of its high throughput, the new sequencer will figure prominently in cancer genetics research and many other investigations that seek the genetic causes of disease,” Mardis says.

In the process used by the new sequencer, genomic DNA fragments and the necessary sequencing enzymes are held in place on microscopic beads nestled into 400,000 tiny wells in a device called a PicoTiterPlate‰. When the plate is placed into the sequencer, sequencing reagents flow over the beads, supplying the necessary components to copy the DNA sequence in a base-by-base fashion.

One of the enzymes on the plate is luciferase, a protein responsible for the glow in fireflies. When a specific base is added onto a DNA fragment, a brief flash of light emitted by luciferase is detected and recorded by the machine.

The sequencer collects data from each bead, and the sophisticated computer and software integrated into the sequencer compiles the data from these reactions to generate 400,000 DNA sequences per 4 hour run of the instrument.

Jeffrey Gordon, M.D., director of the Washington University Center for Genome Sciences, is also very enthused about the instrument’s potential. A major facet of the University’s BioMed 21 initiative, the Center for Genome Sciences helps researchers translate genetic data into new methods of diagnosis and treatment.

As their own research focus, Gordon and his team are developing new approaches for isolating, sequencing and analyzing the genomes of “friendly” bacteria that inhabit the intestine. “The human gut is a bioreactor programmed with at least 800 different species of bacteria,” Gordon says. ” These bacteria have a great impact on human health, and are an integral part of our genetic landscape, but little is known about the gene content of our gut microbial communities. The new sequencer will enable us to obtain essential data about this human gut ‘microbiome,’ rapidly and in a cost-effective way. This effort to decipher the human gut microbiome represents a logical extension of the human genome sequencing project.”

Washington University School of Medicine’s full-time 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 third 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.