Helicos Announced Improved Performance of Its Single Molecule Sequencer

Helicos BioSciences announced improvements in the performance of the Helicos Genetic Analysis System. With these improvements, the system is generating 20 to 30 Gigabases (GB) of high-quality sequence data per run, an output equivalent to the sequencing of seven to 10 human genomes per run. This new performance point generates high-quality data at a rate of 100 to 150 Megabases (MB) per hour. These data are available on the HeliSphere Technology Center, the company’s open access Web site showcasing single molecule sequence data and open source informatics tools.

Having validated the system’s initial commercial performance in September 2008, the company has made the first in a series of planned performance improvements to its patented True Single Molecule Sequencing (tSMS) chemistry that makes better use of the 1GB per hour capacity of the HeliScope Single Molecule Sequencer. In just four months, through better image processing software and a new chemistry formulation, sequencing performance was improved without any changes or upgrades to the system hardware, according to Helicos BioSciences.

These improvements resulted in increases in both the number of usable strands, as well as in the average length and accuracy. System performance is now between 600 million to 900 million strands having an average length of 33 bases, which results in 20 to 30 GB of usable sequence per run. These data are not raw output of the system but the amount of usable data in a specific experiment. The accuracy of these data was improved to a point such that ~99.5% of the usable strands (a%JPY 25 bases with a range of 25 to 55 bases) have a%n 1 substitution error per strand.

Proof of the system’s performance was demonstrated recently by sequencing the 104MB genome of the nematode C.elegans at 27-fold coverage (~2.8 GB of sequence) using just seven of the 50 channels of a single run on a HeliScope Single Molecule Sequencer. Consensus accuracy above 5-fold coverage was 99.999%, or one error in 100,000 bases, which resulted in the identification of hundreds of single nucleotide substitution polymorphisms in the strain sequenced. A sample of 24 predicted polymorphisms were sequenced with Sanger sequencing; all 24 predicted polymorphisms were confirmed. The company is currently undertaking the sequencing of a complete human genome, using its proprietary paired-read approach.

Release Date: February 4, 2009
Source: Helicos BioSciences