Helicos to Debut HeliScope Sequencer by End of Next Summer

Helicos BioSciences will debut its HeliScope DNA sequencer late next summer, the company’s chief executive told investors at a conference last week.

 

The goal is to ship beta instruments at that time, followed by a full commercial launch “soon thereafter,” another company official told GenomeWeb News after the event.

 

This timeline will likely make the HeliScope the fourth next-generation sequencer to be commercialized: 454 Life Sciences will launch its second-generation instrument next spring; Solexa – which disclosed today that it may soon be acquired by Illumina for $600 million in stock — has sold instruments to early access customers; and Applied Biosystems plans to place early-access systems of its APG platform by mid-2007.

 

Helicos, a privately held company that last month won a three-year, $2 million grant from the National Human Genome Research Institute to continue developing its single-molecule sequencing technology, has kept fairly quiet about its technical progress and goals.

 

But Helicos President and CEO Stan Lapidus, speaking at the Rodman & Renshaw 8^th Annual Healthcare Conference in New York City last week, offered some specifics.

 

Version one of the HeliScope is slated to have an output of at least 100 million bases per hour, or at least one billion bases per day, he said.

 

This number only includes sequences long enough to be aligned to a reference genome, Steve Lombardi, Helicos’ senior vice president of marketing, explained by e-mail last week.

 

By comparison, Solexa has said its first commercial instrument will deliver 1 billion bases in around a three-day run; ABI has said its APG platform will initially generate up to 500 million bases per day; while CuraGen recently said 454’s new GenomeSequencer FLX  will create more than 100 million bases in a seven-hour run.

 

Later versions of the HeliScope would have a throughput of more than 1 billion bases per hour, or 10 billion bases per day, according to Lapidus.

 

That throughput could be achieved using flow cells with higher template densities, better assay conditions, and new software, according to Lombardi. The system has been designed and engineered to be able to achieve this higher output of “alignable” sequences, he wrote in his e-mail.

 

Lapidus did not mention the system’s read length, but in response to an investor’s question, he said that “if you can deliver 25 bases on each end of a paired-end ready, you are good,” adding that even shorter reads are satisfactory for tasks like gene expression analysis. “Read length is application dependent,” he said.

 

According to Lombardi, the system’s current mean read length is 27 bases.

 

Helicos, Lapidus pointed out, sees greater market opportunity in medical re-sequencing and other areas that do not require long reads, rather than in de novo sequencing, where longer reads are advantageous.

 

454’s new instrument will provide read lengths of 200 bases or greater, Solexa’s 1G Genetic Analyzer currently creates 25-base reads, and ABI is hoping its first commercial units will deliver 25- to 50-base reads, depending on the template library.

 

Lapidus also touted the HeliScope’s ability to contain cost per base and hour, claiming that the company will be “quite strong” on this.

 

“We will sequence one human genome every 10 days at a cost of less than $10,000 per genome,” he said.

 

That number is “the best estimate we have at this point” for sequencing a human genome at 10x coverage with the first generation flow cell, assay, software, and bioinformatics, according to Lombardi.

 

In addition, Lapidus stressed that Helicos’ single molecule sequencing chemistry will greatly simplify sample preparation since it does not involve making libraries or clones. “We shear and sequence,” he said.

 

The company also has a strategy for paired-end reads that does not require libraries, he said: After reading a stretch of sequence, scientists add a number of “dark,” or unlabeled bases, then resume reading the template with labeled bases.

 

The immediate market for the HeliScope will be academic and pharmaceutical research, Lapidus said, but “the largest application may well be in diagnostics,” he added.

 

So far, the company has disclosed one early-access collaboration, with Jared Roach at the Institute of Systems Biology. ISB President Lee Hood is a member of Helicos’ scientific advisory board.

 

But the company has also been working with Floyd Romesberg at the Scripps Research Institute on improving DNA polymerase, and “will announce a couple of collaborations soon,” Lapidus said last week.

 

Helicos has raised a total of $67 million in funding so far, $27 million in early 2004 and $40 million earlier this year. Investors in both rounds included Flagship Ventures, Atlas Venture, Highland Capital, MPM Capital, and Versant Ventures. The company anticipates another financing round in late 2007 or early 2008 to help commercialize the HeliScope, according to Lapidus.

 

The company has licensed “a fair bit” of intellectual property, he said, including single-molecule sequencing technology invented by Steve Quake at Caltech and published in PNAS in 2003, as well as from other inventors.

 

Though the HeliScope is likely to face some tough competition, Lapidus is confident his company’s single-molecule sequencing platform will stand out from the crowd. “Our data will ultimately speak for itself,” he said.

 

Source from GenomeWeb Daily News