By Kevin Davies

March 5, 2008 | Helicos BioSciences announced today that it has shipped the first ever single-molecule sequencing instrument – the HeliScope – to Expression Analysis, a contract genomic services company based in Durham, North Carolina.

“The first shipment of the Helicos technology signals the next inflection point in the history of medicine,” said Helicos founder, Chairman and CEO Stan Lapidus, in a statement. “We expect the power and performance of the HeliScope system will one day allow physicians to personalize prescriptions, pharmaceutical companies, to cut development times of new drugs and diagnostic laboratories to offer more effective, less expensive tests.”

The HeliScope captures the incorporation of fluorescently labeled nucleotides in single strands of DNA at the rate of more than 1 billion bases per hour. Advantages of this single-molecule sequencing system include its high throughput, relative ease of sample preparation (that dispenses with DNA amplification), and real-time data processing. The platform currently produces 25-megabases of sequence-quality data per hour, which executives believe will increase sharply in the next 12-24 months.

However, the individual strand read lengths are still relatively short, and strands must be sequenced in duplicate to account for artifacts such as the occasional incorporation of “dark” untagged nucleotides.

According to company President and COO Steve Lombardi, Helicos is poised to tap into expansive biomedical research programs such as ENCODE and the newly announced 1,000 Genomes. “Companies like Expression Analysis represent a whole new class of customers who, together with the traditional genome centers, can use our platform to derive in-depth biological meaning from genetic information and enable the use of genetic information in ways we can only imagine today,” he said.

The instrument sells for $1.35 million and comes with a powerful 32-CPU Dell server, which performs real-time analysis of the image data. Kristen Stoop, Helicos’ director of bioinformatics, says, “It does require some effort on [the customer’s] part to think about who is going to use the data, and how it needs to be moved through various levels of access and storage.”

The identity of Helicos’ first customer, Expression Analysis, may come as a bit of a surprise. The company is a contract genomics analysis provider, which provides genotyping, expression, amplification and sequencing services for pharma clients such as GlaxoSmithKline and Lilly, and academic groups including Duke University.

Towards $1000
“What immediately attracted us to Helicos was the accuracy of its single-molecule sequencing offering,” said Steve McPhail, CEO of Expression Analysis. The HeliScope platform “has the opportunity for dramatic performance improvements without significant investments.”

Indeed, according to Helicos executives, the HeliScope is the first sequencing platform on the market that, in principle, could deliver the $1,000 human genome. VP Bill Efcavitch told Bio-IT World recently that the HeliScope could already, in principle, sequence a human genome in two months for under $100,000. And after that?

“We see a technological progression to get to a throughput and cost of a $1000 genome,” said Efcavitch. “We have engineered the reader – the fluor detection part – of the platform, and engineered enough surface area into our flow cells so that we can image and sequence 10x coverage of a whole human genome on two flow cells. To get to that $1000 genome price, you won’t need to upgrade your hardware. It simply changes to 1) the chemistry, and 2) the surface.”