NEW YORK (GenomeWeb) – Ubiquity Genomics, a startup firm on the campus of the HudsonAlpha Institute for Biotechnology in Huntsville, Ala., is commercializing a target enrichment method which allows for capture of regions of interest from a library prior to amplification for short-read, next-gen sequencing.
The firm is also developing the method for longer-read sequencing, and expects to launch a kit for major histocompatibility complex (MHC) locus analysis in the second quarter of this year.
Founded in 2013, Ubiquity Genomics' core technology is a method called Catch-seq, which was described in PLoS One last October.
"It is a way to capture large, contiguous blocks of the genome in a more cost-effective way than, for example, tiling oligos across that same region," Ubiquity Founder Devin Absher told GenomeWeb in an interview this week.
Most commercial target-enrichment products from vendors such as Aglient, Roche NimbleGen, or Illumina "synthesize oligos that tile across a big region," Absher said. "That's cost-effective if you're trying to sequence small, discreet parts of the genome, like exons for example, but it gets expensive if you're trying to sequence a few hundred kilobases or a few megabases."
The Catch-seq method, on the other hand, utilizes genomic clones that have already been determined. For instance, the company can use a BAC or PhOSM clone from the human genome that's already been mapped and sequenced as a template to generate biotinylated probes synthetically, Absher said.
Absher developed this technology out of his own academic research needs at HudsonAlpha.
"I'd been wanting to sequence parts of genes that are not in the coding region, and to enable that, my lab here at HudsonAlpha developed a technology that would be less expensive than oligonuceleotide-based capture," he explained.
The method is particularly useful for epigenetic analyses.
"If somebody were interested in DNA methylation patterns, for example, they're not necessarily interested in the coding parts of the gene, they're interested in regulatory sequences that can be in introns, or they can be 50 kb away from a gene, and sometimes you don't know where those regions are," Absher said.
"To survey the regulatory milieu around a gene, ideally you would sequence large blocks ― you might sequence 100 kb around a gene ― both to find genetic variations but also, you could apply our method to do bisulfite sequencing, or DNAse hypersensitivity assays … where you get both genetic and epigenetic information around that gene," he added.
Ubiquity currently makes custom kits that are "great for short-read next-gen sequencing, like Illumina sequencing," but the company is also developing approaches using the same kits that will be useful for PacBio sequencing, which it hopes to launch in the second quarter of this year.
The method is not patented because it has been published in the public domain, Absher noted, but the company has licensed and improved the efficiency of the technology, and has trade secrets around this development.
Currently Ubiquity Genomics provides custom services enabling primarily academic researchers to do large sequencing projects that include both genetic and epigenetic studies of expansive regions.
The firm plans to launch an off-the-shelf kit to analyze the MHC locus, Absher said.
"That's a 3.8-megabase region with a great deal of genetic diversity, so there's a lot of interest in sequencing that locus," he noted. "Up to now, most people sequence just the exons from some genes [in the MHC locus], but we think there is going to be a great deal of interest in all the non-coding sequence there, in all the regulation that's going on and the epigenetics of that locus."
Absher noted that collaborative academic studies using Catch-seq are likely to be published this year, including one in Nature Immunology.
The company is also sponsoring and participating in the HudsonAlpha-Science Conference on Immunogenomics, which will help it to coordinate its networking with the immunology research community and introduce the MHC locus target enrichment kits, Absher said. It has also reached out to academic communities through email marketing and will begin more aggressive marketing this year.
As a faculty member at HudsonAlpha, Absher also publishes on epigenetics and genomics, including co-authorship of a study last March modeling 3D facial shape from DNA.
But the non-profit institute also incubates multiple small- to medium-sized biotech companies.
"When it was established, HudsonAlpha was designed to be a place where there is both academic and commercial science happening, and that there would be some synergies that could come out of that close proximity. Ubiquity Genomics is an example of that, in that the technology that was developed on the academic side has now been commercialized, and now that company is one of the 15 or 18 commercial companies on the campus."
Other companies on the HudsonAlpha research institute campus include Diatherix and Conversant Bio, which ranked second in a 2011 survey of the top 40 biotech places to work; as well as MDx developer iCubate and immune sequencing outfit iRepertoire, both of which were founded by HudsonAlpha faculty member Jian Han.