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Moore Foundation: $1.6M for Portable Sequencer

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A researcher at the University of Washington and a tech incubator have received $1.6 million from a foundation to develop a portable electronic DNA sequencer.

The Gordon and Betty Moore Foundation made the award to the researcher, who will share a portion of it with the firm, to develop a portable device to identify samples of animals and plants in the field by sequencing short stretches of DNA, so-called DNA barcodes. But the instrument, which will be the size of a grapefruit and cost less then $25,000, might have wider applications, including those in biodefense and forensics, according to its inventors.

The technology will be developed by grant recipient Babak Parviz, a professor in the department of electrical engineering at the University of Washington, and Reveo, a technology incubator based in Elmsford, NY, which will also build and commercialize the finished product.

When developed, the device will read DNA bases electronically using a quantum mechanic effect called electron tunneling, and has the potential to sequence DNA within seconds without amplification, according to its inventors. It could reach beta testing in as little as two years, they say.

The foundation decided to fund Parviz’s research because “the ideas in this grant are different from anything we have seen and have the best potential to lead to a portable device,” according to a spokesman.

Reveo, founded by CEO Sadeg Faris, an inventor and IBM alum with a PhD in electrical engineering, has already developed and spun out a number of technologies; the DNA sequencer will be its first foray in the life sciences.

Once Parviz has successfully demonstrated the ability to read DNA, Reveo will build the instrument. Faris said he hopes within a year to have a proof-of-concept, which would mean the ability to sequence between 10 and 100 bases.

— Julia Karow

Short Reads

Solexa has been making headlines yet again. The company was added to the Nasdaq Biotechnology index as part of a semi-annual update. It also announced plans to seek permission to issue $100 million worth of securities, according to an SEC filing. Meanwhile, Solexa acknowledged that it would not meet its goal of recording revenue from its sequencer in the second quarter of this year; according to CEO John West, an “accounting technicality” will likely delay until the third quarter the company’s ability to recognize revenue from sales of its first early version sequencers. The technicality: first customers should have started to receive instruments by the end of June, but they will have a chance to try them out for a while before having to pay. The machine will list for $395,000.

Chinese scientists released the genome of the Japanese schistosome parasite. The five-year project that sequenced the genome was supported by local and central governments as well as the Chinese Academy of Sciences. The parasite, which is found in contaminated water and can cause schistosomiasis, is prevalent in more than 75 countries, particularly in Asia, Africa, and Latin America.

The Wellcome Trust Sanger Institute together with US and British colleagues published the sequence of human chromosome 1, which is the final chromosome analysis from the Human Genome Project. The actual sequencing was carried out at Sanger, though the University of Washington Genome Center contributed 13 percent of the sequence finishing.

PATENT WATCH

US Patent 7,058,517. Methods for obtaining and using haplotype data. Inventors: Rex Denton, Richard Judson, Gualberto Ruano, Claiborne Stephens, and Andreas Windemuth. Assignee: Genaissance Pharmaceuticals. Issued: June 6, 2006.

This patent covers methods, programs, and resources to analyze and use gene haplotype information. These can measure haplotype frequency in a population, correlations between haplotypes and clinical outcomes, and prediction of haplotype or response to treatment from a gene.

US Patent 7,058,515. Methods for making character strings, polynucleotides and polypeptides having desired characteristics. Inventors: Sergey Selifonov, Willem Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip Patten, Jeremy Minshull, and Lorraine Giver. Assignee: Maxygen. Issued: June 6, 2006.

According to the patent description, this “provides new in silico DNA shuffling techniques, in which part, or all, of a DNA shuffling procedure is performed or modeled in a computer system, avoiding (partly or entirely) the need for physical manipulation of nucleic acids. These approaches are collectively termed Genetic Algorithm Guided Gene Synthesis.”

Datapoint

100

The Joint Genome Institute finished sequencing Methanosarcina barkeri fusaro, marking its 100th microbial genome. The institute’s announcement got a hearty applause at this year’s American Society of Microbiology meeting, held in May.