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SeqLL Plans to Revamp Helicos Technology

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This article was originally published Sept. 29.

NEW YORK (GenomeWeb) – A former Helicos BioSciences employee plans to keep the single-molecule sequencing technology alive through startup SeqLL by offering sequencing services on the HeliScope instrument and revamping the technology.

Earlier this month, SeqLL said it had raised $1 million in a Series A financing round led by Genome Diagnostic Technologies.

SeqLL President Daniel Jones told In Sequence that since founding the company in March 2013, the initial goal has been to "sustain" the Helicos technology and "move it into maintenance mode."

That involved relocating from Helicos' Cambridge, Mass., site to a new laboratory in Woburn, Mass., getting the instruments up and running in the new lab, and beginning to serve preexisting Helicos customers.

Jones said SeqLL currently has between six and 10 employees, including CFO William St. Laurent, who is also CEO of Genome Diagnostic Technologies, and Tisha Jepson, who heads corporate strategy and sales and marketing.

Currently, Jones said, the lab has about six HeliScope instruments running and another 10 in various conditions that would require some effort to get them up and running.

With the new lab established and the technology working, Jones said the next goal is to expand the customer base and also to make improvements to the Helicos technology, focusing on the run time, read length, and throughput.

Helicos went public in 2007 and sold its first HeliScope single-molecule sequencing machine in 2008. Ultimately though, it was unable to sell enough instruments to be commercially viable and filed for Chapter 11 bankruptcy protection in November 2012. In March 2013, the firm sought approval from the bankruptcy court to sell its assets, including its sequencers and reagents, to Jones, who had been a field application scientist. Jones also obtained a non-exclusive license from Helicos to build a new entity that would perform sequencing services and hence, SeqLL was born.

In terms of improvements to the system, Jones said that the initial focus will be to decrease run time to one to three days from seven to eight days.

In the original iteration of the HeliScope, runs were designed to produce a 10x human genome, but going forward, the focus will not be on whole human genome sequencing, but specific applications such as direct RNA sequencing, low-pass sequencing for applications like noninvasive prenatal screening, single-cell sequencing, and other applications that take advantage of the system's single-molecule capabilities and low input requirements, Jones said.

In addition, SeqLL will also work on doubling the read length from around 30 bases to between 50 bp and 60 bp, he said.

Jones said that the company will offer sequencing services and will enable institutions that currently have systems installed to be able to run their machines, rather than producing and selling new machines.

In the highly competitive next-gen sequencing space, SeqLL will face a large hurdle competing with well-established firms like Illumina and Thermo Fisher. Pacific Biosciences, too, has made inroads in the last year, demonstrating that its long reads can provide valuable information. In addition, Oxford Nanopore's highly anticipated MinIon is now in early access.

Nonetheless, Jones said that he thought SeqLL's "sweet spot" would be applications that do not require long read lengths, particularly those that focus on quantitation, and for which sample is limited or degraded, such as from formalin-fixed paraffin-embedded tissue or nucleic acids from single cells.

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