HTG Molecular Launches NGS-based microRNA Assay; Additional RNA, DNA Assays to Follow

By Monica Heger

NEW YORK (GenomeWeb) – HTG Molecular Diagnostics has entered the next-generation sequencing space with the launch of its first assay, which targets and sequences 2,275 microRNAs using its proprietary nuclease protection probe technology.

The assay is HTG Molecular's first product for the NGS space. The firm first told In Sequence it was developing an NGS assay in 2013, after it received a Small Business Innovation Research grant from the National Human Genome Research Institute to make its chemistry — which had previously been used in conjunction with microarrays — sequencing-compatible. At the time, the firm said it was completing phase I of its so called EdgeSeq project and would use the grant for phase II of the project, which combined HTG Molecular's Edge automation platform with an NGS assay.

CEO Tim (T.J.) Johnson told IS that the EdgeSeq miRNA Whole Transcriptome Assay is the first of several NGS-based assays in its product pipeline. It is also developing RNA panels for immunotherapy, FGFR expression, a large RNA-based oncology panel that could include around 3,000 genes, and a comprehensive gene fusion panel for lung cancer. In addition, it will eventually move into DNA-based assays, which are currently in mid-stage feasibility development.

Johnson said that the company decided to move into the NGS space because "our array technology was limited in its dynamic range and sensitivity, which limited the applications for which we could develop products." Next-gen sequencing, meantime, enables the company to couple the front-end benefits of its extraction-free chemistry with the downstream benefits that sequencing provides.

The company chose to commercialize a microRNA panel as its first product because it is a "defined market that is underserved with current products," Johnson said. Profiling microRNA is difficult with current products because they often require high sample inputs and do not always work well with difficult samples such as formalin-fixed paraffin-embedded tissue, Johnson said.

HTG Molecular's nuclease protection probe chemistry, however, eliminates many of the steps that cause bias and that make it necessary to have large sample inputs, Johnson said. The technology does not require DNA extraction, cDNA synthesis, ligation, a selection step, or shearing, he said. "It's truly a lyse and go chemistry protocol."

The product is initially compatible with Illumina sequencing on the MiSeq and HiSeq systems, but the firm will soon launch a version that is compatible with sequencing on Life Technologies' Ion Torrent PGM and Ion Proton systems. There are "minor adaptor changes and things we have to do" before launching on Ion Torrent systems, but "we have run the chemistry and the kits across both sequencing platforms with the same success," Johnson said.

Turnaround time from sample input to final result is between one and one and a half days. And the assay will cost between $325 and $350 depending on volume, Johnson said.

The assay requires 25 ng to 50 ng of RNA, but can also be run directly from a clinical sample. For instance, one 5-micron FFPE section, 12.5 microliters of plasma, paxgene, or serum, or 5,000 cells can also be used as starting sample. The company has not yet established, but is in the process of testing the low-end sensitivity and specificity of the assay. Johnson said the company would publish its workflow soon.

The firm is targeting translational researchers and customers working with miRNA in difficult sample types such as FFPE, as its initial customer base, as well as genomics core labs and translational labs in all settings.

In addition, Johnson said that the firm plans to seek US Food and Drug Administration clearance for at least one of its assays and is aiming for a mid-2015 FDA submission for either 510(k) clearance of premarket approval.

Which assay it ultimately submits will depend on the result of dialog with the FDA around what will be required for the clinical trial design and time to market. He said that although Illumina's MiSeqDx has Class II exempt status, HTG's assay would not qualify as a "same intended use" product, so the firm would not simply be able to register it.

Johnson said that HTG Molecular will compete with companies such as Agilent, Exiqon, and Affymetrix in the microRNA space. As it launches its other products, he said, competition will likely stem from the real-time PCR-based technology.

Eventually, HTG Molecular plans to develop DNA-based assays, which will pit it against numerous firms, including Illumina and Life Technologies.