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Seegene Beta Testing Low-Cost Oligo Service Using Universal Fluorescence System


NEW YORK (GenomeWeb) – In a promotion offered at the American Society of Microbiology Microbe conference last month, Seegene recruited 200 customers to beta test its new oligo service that employs a novel fluorescence system.

The promotion will be followed by an evaluation of the service before going live next year, Helen Cha Roberts, president of the Seegene's US subsidiary, Seegene Technologies, told GenomeWeb this week.

"We had a lot of interest, and we are also going to be targeted in reaching out to other clients we would like to try this service," Roberts said.

Developing the service necessitated the firm creating new software in house, which requires customers to enter an accession number and other information. Similar to typical TaqMan assay design, the site then designs primers and an internal, target-specific probe. The company has the most experience with human, bacterial, and viral sequences, and is working on mouse as well, Roberts said.

The key differentiator of the Seegene SG Oligo method — also called the "universal catcher" system — is that the probe will not have a fluorescent tag.

"Instead it will have a DNA oligo tag that gets cleaved during extension, and cleavage will allow that tag to then hybridize to a complementary sequence on an artificial synthetic reporter," said Roberts.

The reporter contains a so-called Black Hole Quencher, or BHQ, from BioSearch, a firm that was acquired by LGC last year as part of its expansion into the US.

"When the tag hybridizes, it extends and allows the fluorescence to be unquenched," Roberts noted.

Now, customers can buy a tube of the universal reporter and design an assay to a target of choice without creating a target-specific labeled probe, Roberts said, adding that this will keep the cost down, since the most expensive part of an assay really is the reporter dyes. 

"If you are designing for fifteen or thirty different targets, you can use our website to design the probes and primers and then just use the same tube of universal catcher reporter every time," she said.

The firm also makes a proprietary primer type called DPO which adds specificity via having two docking events on each side, Roberts said. This is particularly important with multiplex assays, and is a similar concept to the "SuperSelective Primers" recently described.

Seegene provides custom development services for multiplex assays as well using multiple colors with different tags. It also has 25-plex commercial IVD assays using reporters that have varying melt temperatures. "So, you have five channels of color, and five melting temperatures per channel," she said, noting that this method also requires an endpoint melt-curve analysis.

But the SG oligo technology is really the simplest aspect of the Seegene technology platform, Roberts said. The new software interface then brings the design completely in silico, enabling it to be customer facing. After extensive in-house testing, the firm is confident it works well for singleplex assays, and is now building it out for up to four-plex assay design.

"With the software, we'll be able to offer this at a competitive price to the market ... bringing this technology that we've kept strictly limited to IVD products outside of the US to the mass research market," said Roberts.

The service is targeted to the global market and getting cost down is important, for PCR as a standalone assay or as an orthogonal confirmatory test paired with next-generation sequencing, Roberts said. With the universal reporter used with all targets, it is also easier to troubleshoot, providing "the target specificity of a TaqMan assay with the cost-effectiveness of SYBR Green," she added.

The firm is now looking a price point that is less expensive than TaqMan assays, although the exact pricing remains to be determined.

Seegene has a number of ongoing collaborations using its oligo technologies for IVD projects. Namely, it has partnered with Beckman Coulter, Qiagen, and Becton Dickinson in the last year and a half to develop assays under those firms' brands.

The company is also looking for potential partners in the point-of-care or other markets. "We are not an instrument maker, so we need an instrument partner," Roberts explained, particularly to go through the process of US Food and Drug Administration approval.

The company pursued one such partnership through to approval recently. A test for herpes simplex viruses 1 and 2 was approved that used the Seegene assay design on the Cepheid SmartCyler. That test was submitted in mid 2014, and approved about six months later.

That assay was not ultimately commercialized, however, in part because Cepheid is now focused on newer instrumentation and the assay is lower plex than Seegene would like to pursue, Roberts said. However, it provided the firm with confidence that it can get through the FDA approval process.

The firm is now developing a higher multiplex assay that also includes the HSV 1 and 2 targets, and believes that this assay will be of more interest to the market. In addition, it is working on multiplex gastrointestinal, viral and bacterial respiratory, and genital ulcer panels, and also offers a sexually transmitted infection panel. Some of these assays are also quantitative, and these are typically eight-plex panels, Roberts noted.

The US subsidiary focuses on RUO assays, and for these Roberts said the GI and genital ulcer will be next in the pipeline. "What's nice about RUO is that we can, on occasion, customize the software to allow researchers to read certain pathogens and not all of them" in the panel, she said. The ideal systems for the assays are the Bio-Rad CFX 96 Touch or C1000 Touch, but the firm has preliminary data to show that the Thermo Fisher Quant Studio IV should work as well, "because they have the open software capability that we need and multiple melt curve analysis," Roberts said.

Seegene also began a new joint venture in Mexico earlier this year. The firm's CEO was part of a contingency that joined Korea's president on a visit to Mexico's president, "and there were a lot of business deals that came out of that," Roberts said. The venture will set up manufacturing for SG Oligo and IVD assay development within Mexico, to support the Latin American market.

For the SG oligo service, competition will likely include the entire TaqMan or SYBR Green real-time PCR reagent market. The big players there are IDT, Biosearch, Thermo Fisher, Sigma-Aldrich, Bio-Rad, and Eurofins, Roberts said. But, as far as Seegene is aware, none has anything like the firm's patented "universal catcher" system, she said.