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Microdevice Relies on Tried-and-True Sanger

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Is Sanger sequencing on its way out? Developers of alternative DNA-sequencing technologies might suggest it is, but other innovators believe the technique will evolve much like computers have: from a roomful of expensive and labor-intensive equipment to integrated microdevices requiring little oversight.

In April, a team of academic scientists working with Microchip Biotechnologies, a Dublin, Calif.-based startup founded by three Amersham veterans and a UC Berkeley researcher, published details of an integrated, Sanger-based micro DNA sequencer they developed that fits into the palm of your hand. The company is one of at least three groups trying to lower the cost of and miniaturize Sanger sequencing.

Developers say these devices will cut reagent and personnel costs while maintaining the high accuracy and long sequence reads for which the Sanger method is known. By using tiny amounts of starting material, they also plan eventually to abolish clonal libraries, a cumbersome step in sample preparation, and replace them with bead-based amplification.

At the moment, the technology has enabled its inventors to create a 556-base sequence read with 99 percent accuracy. So far, none of the rival emerging sequencing technologies, like those developed by 454 Life Sciences and Solexa, has published similar read lengths. Such read lengths are required to detect structural genome variations — including repetitive sequences, gene inversions, deletions, and duplications — that play an important role in diseases like cancer, according to Richard Mathies, a professor of biophysical and bioanalytical chemistry at Berkeley.

“This is one of the reasons why we thought it was important pushing Sanger to its ultimate limit,” says Mathies, senior author of the paper, which appears in PNAS.

Microchip Biotechnologies CEO Stevan Jovanovich says he wants to commercialize an integrated, microfabricated DNA sequencer based on Mathies’ developments that includes bead-based template amplification, sample prep, and separation, in 2008.

— Julia Karow

Short Reads

During its quarterly earnings report this spring, Applied Biosystems noted that revenue from its DNA sequencing segment declined 4 percent to $136.5 million. Overall, the company reported an 8 percent increase in sales, buoyed by its mass spec and real-time PCR divisions.

DNAStar introduced its “Rising Star” grant program for small colleges, aimed at helping smaller academic institutions buy the company’s Lasergene sequence-analysis software. Colleges or universities meeting the terms of the program can receive up to $2,500 in matching funds toward the purchase of the software.

454 Life Sciences and distribution partner Roche Diagnostics expect to release the beta version of a new sequencer, called the Genome Sequencer 100, that they say will be better at sequencing larger genomes. Meanwhile, the companies also introduced a new version of the current Genome Sequencer 20 machine that has improved single-read accuracy, software algorithms with additional applications, better reagents, and a LIMS interface.

Reveo, an R&D firm based in Elmsford, NY, announced that it has partnered with the University of Washington to develop a portable DNA sequencer based on nanoprobe arrays. Babak Parviz, director of the Nanosystems Laboratory and a faculty member in the Department of Electrical Engineering at the University of Washington, will lead the university's participation.

PATENT WATCH

US Patent 7,034,143. Systems and methods for sequencing by hybridization. Inventors: Franco Preparata and Eliezer Upfal. Assignee: Brown University Research Foundation. Issued: April 25, 2006.

This patent covers a method related to “nucleic acid probes comprising a pattern of universal and designate nucleotides, or ‘gapped’ probes, and the use of sets of gapped probes in sequencing by hybridization to determine the sequence of nucleic acid sequences. The inclusion of universal nucleotides in the probes allows for efficient and rapid sequencing of longer nucleotide sequences than can be sequenced using traditional probes.”

US Patent 7,041,455. Method and apparatus for pattern identification in diploid DNA sequence data. Inventors: Charles Magness and Dake Sun. Assignee: Illumigen Biosciences. Issued: May 9, 2006.

This provides methods for (1) obtaining two parental allele sequences from diploid DNA sequence signal data, (2) identifying the mutation and haplotype patterns in the two parental allele sequences, (3) assigning likelihood scores for the mutations thus identified, and (4) identifying patterns of methylation.

Datapoint

$8.8 million

Revenues generated by 454 Life Sciences from sales of instruments, reagents, fee-for-service sales, and milestone and royalty payments for the first quarter of this year, up from $1.3 million a year ago.

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