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GnuBio Maxes out New Office Space as it Preps for Commercial Launch

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This story has been updated to clarify GnuBio's commercialization plans.

One week after GnuBio announced that it had expanded into an 11,000-square-foot space as it prepares to enter commercialization, it is already reaching capacity, CEO John Boyce told In Sequence.

The company, which is developing a $50,000 microfluidic sequencer, has nearly doubled its employees over the last year to around 28 and expects to double in size again by the end of next year, Boyce said.

Boyce declined to comment on when it would commercialize its system, although previously the company has said that it would launch by the end of this year.

Currently, the company is looking to hire informaticians, molecular biologists, and engineers. Additionally, it is starting to recruit for a product development team and a vice president of sales, and to expand its manufacturing side.

The new space will also allow the company to fabricate its gene panel cartridges in house, giving it the capability to design customized panels for customers within nine days, Boyce said.

GnuBio's new digs are located in Cambridge, at One Kendall Square, the same business complex as Helicos' previous office, but not the same space, Boyce said.

Boyce said the company is aiming to focus on the gene panel and CE sequencing markets and plans to announce several gene panels targeting between 50 to 200 genes within the next couple of months.

The system is based on "picoinjector" technology developed in co-founder David Weitz's physics laboratory at Harvard University (IS 10/4/2011).

Genomic DNA is first sheared into 1-kilobase sized fragments, and then a picoinjector injects amplified DNA into microdroplets that contain a pair of PCR primers that represent the amplicon to be sequenced.

After the DNA is enriched, a second picoinjection transfers the droplets into sequencing probe droplets that are barcoded with fluorescently labeled hexamers. Only hexamers that match exactly hybridize to the DNA and act as primers for DNA polymerase, enabling the sequence to be read.

GnuBio has designed a library that contains 4,096 hexamers — all possible six-base combinations — plus a collection of longer probes to capture homopolymers and repetitive sequences a total of around 5,000 probes.

Sequence is read by first doing a local alignment, where both the true matches and negative matches are used to distinguish true variants.

Boyce said that since February, when the company presented at the Advances in Genome Biology and Technology meeting in Marco Island, Fla., the company has increased the number of dye barcodes it uses to identify each probe from 300,000 to 500,000 (IS 2/28/2012).

The increase in barcodes will help the company increase its read lengths and also move into other applications, such as proteomics and analyte interrogation, Boyce said.

For now, though, the company plans to focus on sequencing and is looking to target the gene panel and CE market, Boyce said.

The system can detect alleles with a frequency as low as 1 percent. Sequencing for a 50-gene panel takes three and a half hours, with an all-inclusive cost of around $40 per sample, Boyce said.

While variant calling and analysis are done in real time on the box, the company currently does not do interpretation, but Boyce said it is looking to partner with another company to offer those services.

Aside from gene panels, Boyce said the company is also looking to do hotspot interrogation, and said that it could analyze over 700 hotspots in just half an hour.

Boyce said that within the next month or two, the company will disclose several of the gene panels it plans to first commercialize. So far, it has been working with the Montreal Heart Institute and City of Hope Molecular Diagnostic Laboratory, as well as other unnamed collaborators, Boyce said.

The Montreal Heart Institute previously had an early access system, which, as reported by sister publication PGx Reporter, it used for a pilot project to develop a gene panel for sudden cardiac death (PGx Reporter 2/1/2012). Following the completion of the pilot, the system was shipped back to GnuBio.

While the company is looking to target the clinical market, Boyce said that the technology will have applications in the research market as well, particularly for reference labs and researchers who want to do sequence validation or to design panels as a follow-up to a genome-wide association study.

Competitors will be primarily Life Technologies, both its CE business and its Ion Torrent PGM platform, which some clinical laboratories have started to adopt for amplicon sequencing. The system could potentially also compete with the Illumina MiSeq, which is also starting to make inroads into the clinical market.

Boyce said he does not think that nanopore sequencing systems, such as the ones being developed by Oxford Nanopore, would be immediate competitors because nanopore sequencing is still an unproven technology and its error rates are too high to be used in a clinical laboratory.

GnuBio is also looking to eventually gain US Food and Drug Administration 510(k) clearance for its system, likely by partnering with a diagnostic company on assay design, said Boyce.

He said that he has had conversations with the FDA and that the agency especially likes the fact that the GnuBio platform is a closed system, with each step from PCR amplification to sequencing and analysis all done on the same cartridge, minimizing the opportunities for contamination or mixing samples.

Large diagnostics companies have also expressed interest in submitting a diagnostic test on the GnuBio system for 510(k) clearance, he said.

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