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Helicos Sees Five to 10 Orders By End ‘08, Shows Resequencing, Gene-Expression Results

Helicos BioSciences said last week that it expects to have between five and 10 orders for its Helicos Genetic Analysis system by the end of this year.
In the meantime, the company is testing the performance of its system for applications such as bacterial genome sequencing and gene-expression analysis.
Helicos President and CEO Steve Lombardi told investors and analysts at the UBS Global Life Sciences Conference in New York last week that the firm anticipates a total of 15 to 30 orders for its system by mid-2009. He said Helicos currently has 13 instruments in various stages of assembly and testing at its factory, and noted that eight of the machines are at a point in the production process that they can run customer samples.
The company has received two orders for its system so far. In February, Expression Analysis became the first customer to order the platform (see In Sequence 3/11/2008).
Last month, Helicos said that it had received a second order from an unidentified US cancer center. Lombardi said last week that Helicos expects to ship that second instrument on Oct. 1.
As of the end of the second quarter, Helicos had yet to book revenue from the sale to Expression Analysis. Asked during the question-and-answer session last week about timing for receiving payment from customers, Lombardi said that although payment would normally come after installation of the system, because Helicos is offering a new technology, it has to prove to customers that the system performs as advertised.
Lombardi compared the cost of the Helicos Genetic Analysis System with that of an unidentified competitor in the second-generation DNA-sequencing market. Though the $1.35 million list price of Helicos’ system is significantly higher than those of its competitors — Illumina, Applied Biosystems, and Roche/454 — Lombardi argued that the total cost of ownership, when taking into account additional costs such as sample prep and reagents, is similar to that of its competitors.
Asked by an audience member how the HeliScope will compete against the newest version of ABI’s SOLiD sequencer, which ABI plans to announce this week (see related article in this issue), Lombardi said the HeliScope’s “combination of benefits will make us a winner in the marketplace.” The company cites easy sample preparation, high ultimate throughput, low reagent costs, and a low error rate due to a lack of sample amplification as the main advantages of its single-molecule sequencing technology.
Lombardi acknowledged, though, that the firm “lost six months of time,” during which customers purchased competing systems, due to a reagent-instability problem. The problem impacted sequencing performance and limited the firm’s ability to generate data and secure additional orders. Lombardi said previously that the reagent issue has been solved (see In Sequence 8/12/2008).

“We are not quite sequencing a human genome yet.”

In the meantime, the company is testing the performance of its system in-house for a number of applications.
“We are not quite sequencing a human genome yet,” Patrice Milos, Helicos’ chief scientific officer, said during a presentation last week at the Cambridge Healthtech Institute Exploring Next-Generation Sequencing conference in Providence, RI. Within six to 18 months, however, the company hopes to be sequencing human genomes.
Milos showed data from an E. coli genome-sequencing project that used the same pipeline that Helicos intends to use for human candidate gene resequencing.
Company researchers generated 181 megabases of total E. coli data, or about 35-fold coverage of the unmasked genome, in a single flow cell channel. After mapping the reads to the genome, they found areas of low coverage, mainly in regions that are known to be repetitive or closely related to others. However, coverage of areas with different GC-content was “relatively homogeneous,” and independent runs on different HeliScope instruments correlated well.
The scientists also sequenced two other bacteria — one with high and another with low GC-content — and found that their genomes were covered similarly to the E. coli genome, which “bodes well for sequencing a human genome,” according to Milos.
Since the two flow cells of the system have 50 channels in total, 50 bacteria could be sequenced in a single eight-day run on the system, she pointed out.
Digital gene expression is another application that is “available to customers today,” according to Milos, and the company has run both yeast and human mRNA samples on its instrument. In order to test the reproducibility of the sample prep, three company scientists prepared samples from the same source of mRNA side-by-side and obtained “highly correlated” results, she mentioned.
Tal Raz, a group leader and senior scientist for methods development at Helicos, presented results from a transcriptome analysis of the yeast S. cerevisiae during a separate talk at the CHI conference.
On a prototype instrument, company researchers generated 5.1 million filtered reads. They aligned 3.4 million of these to the yeast transcriptome, while 1.7 million reads did not align and were used for a cluster analysis that discovered novel transcripts and alternative splice sites. The scientists observed “low channel-to-channel variability” and “good agreement with microarrays,” according to Raz. They were also able to discover more than 1,000 sequence variants between two yeast strains.
Helicos has also used its system to analyze two standardized samples that were generated several years ago for the MicroArray Quality Control, or MAQC, project. These samples have been extensively characterized both by microarrays and by qPCR. The researchers found “high agreement between predicted and observed counts,” Raz said.
Within three to six months, the company plans to generate full human transcriptome sequences using 10 channels of a flow cell, according to Milos.
She mentioned that the company is making software and datasets for its sequencing system available to researchers on Open Helisphere, a wiki that also hosts Helicos open source projects.
Milos also said that Helicos has generated sequence data for the Broad Institute and is waiting to hear back from the institute.
While Helicos generates scientific data and awaits more orders and revenue from customers, its cash is diminishing. As of June 30, the company had $24.4 million in cash and $10.5 million in restricted cash. CFO Stephen Hall reiterated last week that the firm plans an “opportunistic funding” by the end of the first quarter of 2009, with an eye on limiting dilution of its stock.

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