This article has been updated with additional information.
Helicos BioSciences booked its first instrument revenue during the first quarter and has received commitments for two more instrument placements from undisclosed sites, which it expects to install by the end of June, the company said last week. The new orders will bring the total number of installments to five.
During the first quarter of 2009, Helicos booked about $1.2 million in total revenue, consisting of $829,000 from the sale of an instrument that it shipped in 2008; $134,000 for proprietary reagents sold to customers in the first quarter; and $239,000 from a National Institutes of Health grant, according to a filing with the US Securities and Exchange Commission.
Helicos did not disclose the source of the instrument revenue, but it only shipped two sequencing systems last year, one of which was returned earlier this year without payment. The other one was shipped to Stanford University last October (see In Sequence 10/7/2008), where Helicos scientific co-founder Steve Quake, a professor of bioengineering at Stanford, recently used it to sequence his own genome (see In Sequence 3/10/2009).
Helicos spent $4.1 million on research and development during the first quarter, down from $5.7 million in the first quarter of 2008, "as we focused more of our efforts on manufacturing activities and spent less time on research and development activities," according to the SEC filing.
R&D activities focused on maintaining and enhancing the initial version of the Helicos system and developing "new and different genetic analysis assays, which will extend the capability of the initial version."
The company's net loss totaled $6.5 million, down from $11.8 million during the year-ago quarter.
Helicos ended the first quarter with $13.9 million in cash, down $5.8 million from the end of 2008. The company reiterated that it expects to be able to maintain its operations with its remaining cash and revenues into the first quarter of 2010. Sometime before then, it said, it will have to raise additional funding "through public or private equity or debt financings or other sources, such as collaborations and licensing arrangements or partnerships."
In its statement last week, Helicos said that is has placed its Helicos Genetic Analysis System at three user sites so far. Besides Stanford University, the Broad Institute and the Dana-Farber Cancer Institute have received instruments, which were both installed earlier this year.
The company also said that it has received commitments for two additional instrument installations, which it plans to make during the current quarter. Helicos did not name the customer sites, but earlier this year, the firm said it had received an order from the St. Laurent Institute for an instrument that was to be shipped to the University of Maryland (see In Sequence 4/7/2009).
Helicos said that two of the five installed or soon-to-be-installed instruments "have been purchased by customers", while three have been "designated as reference site installations at institutions for scientific and commercial evaluation."
The company said that future shipments of its system will be "subject to various customer evaluation periods with acceptance criteria," which it expects to last beyond the fiscal quarters in which it ships a unit.
Helicos also mentioned in its statement last week that it has recently received more requests for quotes, which it attributed both to the performance of its technology and to new funding opportunities from NIH as part of the American Recovery and Reinvestment Act.
The company said it is "actively working" with customers on grant applications for research programs "that will benefit from the HeliScope platform."
In addition, the firm said that its scientists as well as customers and collaborators are beginning to submit studies for publication that used the Helicos single-molecule sequencing technology.
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Collaborators have already started to present results from Helicos sequencing projects at scientific conferences: at the Biology of Genomes meeting at Cold Spring Harbor Laboratory earlier this month, a researcher from the Broad Institute presented a project on analyzing origins of replication in yeast (see In Sequence 5/12/2009).
In posters at the same conference, researchers from Boston University presented data from Helicos and other sequencing platforms to determine copy number variations in the human genome; and Helicos' chief scientific officer, Patrice Milos, showed results from a collaboration with Cold Spring Harbor Laboratory to analyze short RNAs in humans.
Helicos also updated performance specifications for its instrument last week. As of this month, it said, the system can deliver up to 170 "useable" megabases per hour with DNA samples; up to 20 million "useable" reads per channel, translating to a billion reads per run; and up to 33 "useable" gigabases per run.
The median read length for the Helicos system is now 33 bases, "with accurate reads up to 55 bases," and the error rate is 3.5 percent, which includes a 0.25-percent substitution error rate.
By comparison, Illumina's latest specification sheet for its Genome Analyzer IIx states an output of up to 25 gigabases per 9.5-day run, with paired reads up to 75 bases in length, and up to 21 million reads per channel, or 168 million reads per run. The instrument's per-base read accuracy can reach more than 99 percent. By the end of the year, Illumina plans to increase the output to 95 gigbases per run.
Applied Biosystems supports an output of up to 30 gigabases per run with 50-base paired reads for its SOLiD 3 system, and up to 600 million reads per run, which takes up to 14 days, according to its latest specification sheet. Due to its two-base encoding scheme, the "system accuracy" exceeds 99.94 percent, according to the firm. By the end of the year, ABI plans to achieve up to 100 gigabases per run.
Helicos said that the average cost of generating data on the instrument can be as low as 45 cents per megabase, but it did not specify what is included in this cost.
The company said it has "demonstrated technical feasibility" for sequencing RNA directly, and for sequencing DNA and RNA from degraded samples, which it said will be important for analyzing DNA and RNA from stored tumor samples.
Helicos is now also supporting RNA sequencing, copy number variation analysis, ChIP-seq, and small RNA analysis as new applications, and reiterated that it plans to make paired-read sequencing available to customers during the second half of 2009.
Leerink Swann research analysts downgraded their rating for Helicos from "outperform" to "market perform" this week, citing the company's "near-term funding challenges," and "slower-than-anticipated ramp in HeliScope sales," despite its technical improvements.