October 1, 2006 (Vol. 26, No. 17)
Solexa Says its Novel System Offers Better Cost-effectiveness via Use of Short-read Sequences
Solexa (www.solexa.com) claims that its new technology will transform sequencing by reducing cost and increasing throughput. “Our technology will offer a hundred-fold improvement in productivity and a hundred-fold reduction in cost, a combination that no other sequencing platform has offered to date,” says Omead Ostadan, vp of marketing at Solexa.
The new system, the Solexa Genome Analysis System, offers a novel approach for genetic analysis and functional genomics. The platform generates one billion bases per run and could potentially allow researchers to sequence a human genome for $100,000. No other sequencing technology has yet achieved this milestone.
The Solexa Genome Analysis System includes the 1G Genetic Analyzer, the Solexa Cluster Station, dedicated reagents and consumables, and a complete suite of data collection and application analysis software. The genetic analysis system combines massively parallel short-read sequencing using Solexa’s Clonal Single Molecule Array™ technology and reversible-terminator sequencing chemistry.
Randomly fragmented genomic DNA is attached to the internal surface of an eight-channel flow cell. The single molecules of DNA are then amplified into clonal clusters. Up to 1,000 identical copies of each single molecule are created in close proximity, and cluster density can reach up to 10 million single molecule clusters per square centimeter. Each channel of the flow cell can yield up to 5 million distinct clusters and generate more than 125 megabases of sequence data. Researchers can analyze up to eight distinct samples per flow cell.
The millions of DNA clusters present on the flow cell surface are then sequenced by Solexa’s Sequencing-by-Synthesis technology, which uses four fluorescently labeled modified nucleotides. Built into these nucleotides is a unique reversible termination property. The sequencing reaction occurs in the presence of all four nucleotides, allowing the polymerase to select the correct base to incorporate in each chemistry cycle. The natural competition among nucleotides leads to higher accuracy than in methods where only one nucleotide is present in the reaction mixture at a time.
After each chemistry cycle, the 1G Genome Analyzer images the clusters through a series of digital photographs. After reversing the termination step, the instrument executes another chemistry cycle, allowing another base to incorporate, and then introduces all four bases to extend the DNA by one more base. The instrument alternates cycles of chemistry and imaging until the desired read length has been achieved.
The core of the Solexa technology is based on short-read, high-quality sequences. “The system has the potential for dramatically improving the cost and efficiency of a variety of experiments,” says Ostadan. “We are developing the system for a number of key applications, including whole-genome sequencing, expression profiling, and small RNA discovery.”
In time, the technology could be used for other applications, such as whole-genome methylation analysis, chromatin immunoprecipitation assays, and other assays that require enzymatic cleavage and subsequent sequencing of tags. Moreover, researchers can use the same instrument to carry out all of these applications. “That’s very appealing, especially for core facilities that cater to a diverse set of customers and applications,” Ostadan adds.
The Solexa Genome Analysis System can generate sequence-based genome-wide expression profiles of transcripts derived from any gene of any species without prior knowledge of that species’ transcriptome. This makes the technology ideal for analyzing organisms with poorly annotated genomes or for discovering transcripts in well-annotated genomes.
In addition, few discovery tools exist today for biotechnology and pharmaceutical researchers who study the role of small RNA in the control of regulation. The new system fills that void for expression profiling of small RNA, Ostadan notes.
The system will complement association studies and genotyping experiments that rely on panels of SNPs, for example, the HapMap SNP set, predicts Linda Rubinstein, CFO. Although HapMap represents a useful starting point for understanding sequence variation, a more comprehensive understanding of sequence variation is needed. “The future lies in capturing all the variation rather than sampling parts of it,” she says.
Although several companies have created products that offer panels of these predefined SNPs, based on the HapMap Project, Solexa’s Genome Analysis System can help researchers interrogate all the bases in a human genome. For instance, thousands of samples from diabetes patients could be screened to find SNPs that are linked to the disease.
However, “typically the SNP itself is not the causative mutation,” Rubinstein cautions, and a more intensive sequencing effort will be required to investigate any candidate SNPs that emerge. “Our technology is perfect for that complementary approach,” Rubinstein says.
The large amounts of information obtained from sequencing individual genomes will also speed the progress of personalized medicine, since current methods are costly and provide insufficient data about the genetic basis of common human diseases and individual responses to drugs.
To further demonstrate the utility of the Genome Analysis System, Solexa researchers also plan to sequence the genome of an anonymous person in 2006. The project is expected to take a few months, in contrast to the Human Genome Project, which took years to complete.
As a result of the Human Genome Project and an independent sequencing effort by Celera (www.celera.com), “we have only two complete sequences in the world today,” says Rubinstein. Although those two complete human sequences were a major scientific accomplishment of the 20th century, Solexa wants to sequence a third human genome using the Genome Analysis System. The sequencing will take place in just one laboratory and will be completed in less than a year. “That’s extremely exciting to people who work in this area,” says Rubinstein.
The Solexa Genome Analysis System will significantly improve productivity at large sequencing and expression centers, core facilities, and individual laboratories. The system is expected to be able to sequence 1 billion bases in approximately two days by the end of the year, enabling a 3 billion-base human genome to be sequenced at 25-fold coverage in two to three months, according to Rubinstein.