DNA sequencing has evolved through two generations and is now on its third, with technology providers racing to sequence a complete genome for $1000 or less. In March 2009, the cover article of this magazine provided a glimpse into many of the top sequencing technology providers. This article provides an update on these companies, their main sequencing platforms, and how close we are to reaching the first $1000 human genome. 

Life Technologies
The SOLiD sequencing platform from Life Technologies (Foster City, Calif.) can be described as next-generation sequencing, specifically, Gen2 next-generation sequencing and as a technology with many strengths. “The first key strength to the SOLiD system is that genomes are read off of small (one-micron) magnetic particles where short fragment libraries are amplified onto the particles,” says Gina Costa, PhD, senior director of the SOLiD Program at Life Technologies.  “The second key strength is that the SOLiD system uses ligases, not polymerases, to sequence genomes ... this allows template strands to be read multiple times by multiple reporter sets ... and this, in turn, serves to reduce both systematic and basecalling errors and increase overall basecalling accuracy.” In addition, the SOLiD system can also sequence both DNA, and importantly, RNA, where strandedness information is retained. It is this combination of genome information that provides a very powerful tool for biological discovery, including pharmaceutical discovery.

Current SOLiD chemistries enable users to sequence 60 gigabases per run—typically 14 days—which is somewhat slower than third-generation sequencers. A major reason for the longer turnaround time is that the current upfront workflows in preparation for an instrument run are manual. “Given SOLiD throughputs are to be increased to 300 gigabytes this year, automation solutions for SOLiD sample preparation will also be released in 2010.”

Agilent Technologies
In February 2009, Agilent Technologies (Santa Clara, Calif.) had just launched the SureSelect Target Enrichment System, which is a line of products based upon a hybrid capture method. At that time the product was in the hands of several early access users, but its use is now widespread. SureSelect was originally launched to work with the Illumina sequencing system for their single end sequencing protocol. “When we were developing the first version of SureSelect, Illumina sequencers would only yield 35 base reads with end-sequencing, yet as we were developing, paired-end read capabilities were being developed and adopted, so SureSelect needed to go through a rapid protocol expansion to address the needs of these users,” says Fred Ernani, PhD, senior product manager of emerging applications for Agilent Technologies, who adds that “Agilent launched SureSelect products to address the needs of researchers running paired-end sequencing [in September 2009] and, as such, these researchers are further enabled to take advantage of the increased efficiencies in data analysis that paired-end sequencing brings Illumina customers.”

More recently, the SureSelect Technology was also adapted to work with Life Technologies’ SOLiD sequencing platform. Another reason for the development of SureSelect is that NextGen sequencing technologies are not targeted, i.e. they are based on shotgun sequencing across the entire genome. So by enriching for only those sequences of interest prior to sequencing, the SureSelect platform enables researchers to reduce the time it takes to complete a sequencing project as well as the cost of the project. In 2009, Agilent Technologies also recently released the SureSelect Human All Exon kit that targets human exons and is available for both Illumina GA and SOLiD.

click to enlarge Demonstrating the principle of detection for Pacific Biosciences SMRT system. (Image: Pacific Biosciences)

Pacific Biosciences
Last March, Pacific Biosciences (Menlo Park, Calif.) was planning the commercial launch of its third-generation sequencing platform: Single Molecule Real Time (SMRT) System. In 2010, the company is much closer to achieving that goal. “We will provide a system that is on par with second generation in terms of throughput and cost, but it’s going to be dramatically better in terms of read length, amount of time to result, and other features,” says Steve Turner, PhD, founder and chief technical officer of Pacific Biosciences. “With our current technology, we’ve shown read lengths of up to 3000 bases and we expect to push that up to read lengths of 50,000 bases,” he says.
 
Although the 2010 system is impressive, Pacific Biosciences promises an even stronger follow-up in 2014. “We intend to introduce another instrument in 2014 capable of sequencing an entire human genome in a matter of 15 minutes for $100,” says Turner, who adds that a tremendous amount of work must be done between now and then to make the data useful to pharmaceutical companies and others.

Complete Genomics, Predictions
In March 2009, Complete Genomics (Mountain View, Calif.) was planning the validation of its third-generation sequencing platform. Today, it has sequenced more than 50 human genomes and is preparing for the launch of a commercial service. Says Clifford Reid, MBA, PhD, chief executive officer of Complete Genomics: “Third-generation technologies are driving down sequencing costs to the thousand-dollar level per human genome.”

“Eventually it will cost $1000 to sequence a complete human genome, but that’s going to take a few years,” says Reid, who adds that his company plans to be the first to ship thousand-dollar genomes. “When most companies talk about the thousand-dollar genome, they talk about $1000 in reagent costs. We talk about $1000 in total price.” And this eventual cost reduction can be directly attributed to technology: DNA nanoarrays. Complete Genomics is able to pack more DNA onto one of these semiconductor-based arrays, which drives down the cost per base of DNA sequenced. The other cost reduction: Complete Genomics patterns these arrays with a perfect grid of spots, which enables them to image the arrays very efficiently.

Reid predicts that Complete Genomics will impact the pharmaceutical industry in two main ways. “In the diagnostics space, our technology is making it economically feasible to run large complete human genomes in sequencing studies to look for new biomarkers. This will enable them to expand the search for biomarkers beyond common variants (SNPs) into more complex and rare variants that are likely to have much more power as biomarkers or companion diagnostics for therapeutics, says Reid. “The second area is that this will enable new pathway discovery. So, for the first time, researchers will be able to identify on a systematic basis the causal variants underlying genetic diseases.”

About the Author
James Netterwald is president and CEO of BioPharmaComm LLC, a provider of writing, editing, and consulting services to the life science, pharma-biotech, and public relations industries.

This article was published in Drug Discovery & Development magazine: Vol. 13, No. 3, April 2010, pp. 14-15.