Faster, Cheaper Sequencing & Drug Discovery Drive HGP Commercialization

From the Archives, SEPTEMBER 1, 1995

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EDITOR’S NOTE: In 1990, Congress established funding for the Human Genome Project (HGP) and set a target completion date of 2005. The International Human Genome Sequencing Consortium (IHGSC) reported the first rough draft of the human genome sequence in June 2000, and the HGP published the first analysis of the human sequence in 2001. The IHGSC announced an essentially finished version of the human genome sequence in April 2003. This September 1995 GEN article suggests where the research effort stood at the time.

From the Archives, SEPTEMBER 1, 1995As the physical map of the human genome nears completion, efforts to sequence the genome’s three billion base pairs as quickly and cheaply as possible intensify. Five years ago, When the Human Genome Project (HGP) began, sequencing was a manual, labor-intensive process, prohibitively expensive on a large scale (multiple dollars per base) and requiring the use of radioisotopes.

Semi-automated instruments, such as those made by PerkinElmer’s Applied Biosystems division, Pharmacia, and LI-COR, have simplified the sequencing task. Using alternative sequencing technologies, some companies now boast of the ability to sequence 7,000–9,000 base pairs per hour, at a cost of $.05-$.10 per base. And that is just the beginning, note these companies, as they race to achieve longer runs per sample and more samples per machine or device.

Hyseq recently announced the ability to read 64,000 bases in a single reaction.

“The significance for discovery of genes is that there will be a lot less subcloning required and we will be able to look at much larger pieces of the genome,” says Lewis S. Gruber, president and CEO of Hyseq. “With respect to diagnostics, we can look at multiple genes—those don’t have to be 64,000 contiguous bases.”

For example, in a single sequencing run, such a high-throughput system could analyze polymorphisms among multiple individuals and the way they affect the phenotype.

“We are at the point where the technology will allow us to begin to undertake the first genome sequence,” Carol Dahl, PhD, program director of the sequencing technology branch of the National Center for Human Genome Research, tells GEN. “Now the big emphasis for increased efficiency is that of systems integration.”

Manual intervention

Although the electrophoresis and data collection aspects of DNA sequencing have become highly automated, much manual intervention is still required upstream and downstream of these two processes. “What we want to see is a more complete systems integration where you have automation taking you from putting in your sample—actually having automated sample preparation that feeds directly into the sequencing—and also data analysis,” says Dahl.

Substantial increases in throughput and reductions in cost will result from advances in four aspects of sequencing technology according to Dahl: increased automation, systems integration, reductions in scale, and increased parallelization. The HGP is looking to fund improved electrophoretic technologies, in particular, capillary electrophoresis and ultra-thin gels.

“We are still funding applications and grants on alternative technologies, so we remain interested in the prospects of mass spectrometry and some single-molecule approaches to DNA sequencing. But we think that may be beyond the first human genome,” she says. “It’s important to keep in mind that a lot of the technologies that are coming forward for the HGP are going to have broader DNA analysis applications. This is going to be a big market opportunity, and I imagine industry will really jump on board quickly.”

Additional markets

Industry has indeed envisioned the
opportunity for DNA sequencing and analysis instrumentation beyond the HGP and is setting its sights on markets that include clinical diagnostics, environmental testing, industrial process monitoring, forensics, and agriculture.

Research efforts are moving from gene structure, or sequence data, to gene function,” according to Frank Ruderman, president and CEO of Genomyx. “Now we have to figure out the function of these genes—by animal type, by tissue, and by stimulant.”

Ruderman expects differential display to emerge as the technique of choice for gene function analysis. Sequencing and differential display gels provide information that differs in both content and utility. “Sequencing data provide you with the [gene’s] blueprint. Differential display tells you how it operates,” he says…