This article has been updated from a prior version to include additional information.
Helicos BioSciences has reduced the price of its single-molecule Helicos Genetic Analysis sequencing system by about 25 percent to $999,000, company officials said at the JPMorgan Healthcare Conference in San Francisco last week.
Helicos has also received an order for the instrument from the University of Maryland, the company's third customer since it launched its instrument at the beginning of last year, according to the officials.
The original price of the Helicos Genetic Analysis system, which includes the HeliScope Single Molecule Sequencer and the HeliScope Analysis Engine for data storage and analysis, was $1.35 million, making it the most expensive next-generation sequencing system on the market. Sequencing platforms from Roche's 454 Life Sciences, Life Tech's Applied Biosystems, and Illumina have list prices on the order of $500,000.
In terms of attracting new customers, Helicos will "at least initially" narrow its focus on cancer centers, according to CEO Ron Lowy, who took the helm of the firm in December (see In Sequence 12/2/2008).
"We feel like they are in the best position, in the short run, to take advantage of the technology and the capabilities that are there," he said during his presentation, which was webcast.
In a Q&A session following his presentation, he added that these centers will likely be not as affected by the ongoing financial turmoil as other potential customers, such as pharmaceutical and biotech companies.
In addition, Helicos is planning to partner with other companies "where appropriate" in areas such as distribution, manufacturing, or services that are "not necessarily our expertise," he said.
Lowy told conference attendees that Helicos, which raised $18.6 million (see In Sequence 12/23/2008) in a private placement of shares in December, paid off $13 million of a $20 million loan from GE and ended the year with $20 million in cash.
Based on its current burn rate, this will support the firm through 2010, he said, adding that Helicos expects to approach cash-flow breakeven in early 2010.
"We have enough money to do what we need to do," according to Lowy.
Helicos shipped its first instrument to a customer, service provider Expression Analysis, last March (see In Sequence 3/11/2008). In October, the company shipped an instrument to Stanford University (see In Sequence 10/7/2008), and in December, it said it will place an instrument at no cost at the Broad Institute (see In Sequence 12/23/2008), which Lowy said will be installed by the end of January.
According to Lowy, instruments at customer sites are now beginning to deliver performance similar to Helicos' in-house systems.
"That's been one of the real issues at Helicos, is that we see this wonderful performance in-house, and now we are starting to see that with the systems that we delivered to the field," he said.
Helicos Chairman and Co-founder Stan Lapidus told the audience that for the last three months or so, the instrument has been delivering up to 140 megabases of data per hour for customers and collaborators at a cost of about $0.75 per megabase. He said the tool averages an error rate of under 5 percent, a substitution error rate on the order of 0.5 percent, and has a median read length of 33 bases.
"Just recently," he said, the company developed an improved rinsing chemistry that decreases the background of the images the instrument takes during the sequencing process and yields an additional 30 megabases of data per hour, or 33 gigabases per run, which takes eight days.
The error rate, he said, has been reduced to 3.5 percent, and the substitution error rate to between 0.2 and 0.3 percent. For "contract customers," he said, the cost per megabase will now be $0.45.
For comparison, Illumina, also presenting at the conference, said its Genome Analyzer now generates up to 3 gigabases per day, or 125 megabases per hour. According to a systems specifications sheet on the company's website, the system has a per-base accuracy of greater than 98.5 percent.
Life Technologies said last week that its Applied Biosystems SOLiD 3.0, which will be launched next month, will generate up to 20 gigabases of data per run. The company's specifications sheet calls the system's accuracy greater than 99.94 percent "due to 2-base encoding," but does not list the raw accuracy.
Neither company lists the cost per megabase of data generated on their respective system. However, Lowy said the Heliscope, when compared to competing second-generation sequencing systems, has at least a 10-fold cost advantage for sample preparation, which costs between $1 and $25 per sample. He also said the platform has an unspecified advantage on the cost per megabase of data and the cost per system "compar[ing] apples to apples." He did not elaborate.
The latest list prices for the Illumina Genome Analyzer and the ABI SOLiD were not immediately available, but in the past, these instruments had list prices of between $500,000 and $700,000.
In addition, the sample prep of Helicos' system is easier and faster than that of competing systems, Lowy claimed, involving fewer steps and reagents.
Because there is no need to amplify the DNA prior to sequencing, the system shows "virtually no" GC bias, according to Lapidus, so more coverage can be achieved from regions that are poorly amplified with the same amount of sequencing, compared to other systems.
"This extra coverage, we believe, gives the Helicos system a permanent advantage," he said.
Going forward, the company will have "an execution focus," Lowy said. "This is doing what we say we are going to do. We've got a history of maybe not quite doing that."
— Edward Winnick contributed reporting for this article from Helicos' Q&A session at the JPMorgan Healthcare Conference in San Francisco.