NEW YORK (GenomeWeb) – Signaling a push into the clinical laboratory market, Agena Bioscience announced today the launch of a 24-well format of its MassArray system. The new format is tailored to smaller clinical labs and costs at least $100,000 less than larger versions of the platform.
The firm is now positioning MassArray as a complement to next-generation sequencing and developing additional products to tap into the liquid biopsy market, Peter Dansky, CEO of Agena, told GenomeWeb in an interview.
The new 24-well format adds to Agena's existing MassArray portfolio, which was acquired from Sequenom when that firm divested its biosciences division last June. Agena, meanwhile, was created by healthcare private equity firm Telegraph Hill Partners.
The firm initially acquired MassArray because it is "a well established platform in the research market," Dansky said, adding, "What we saw was a great, proven research tool that is really ready for clinical diagnostic applications."
MassArray uses matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, better known as MALDI-TOF, for detection of nucleic acids. The platform is about 20 years old and has been cited in over 2,000 peer reviewed journals, according to Agena's website.
As part of orienting to the clinical market, the firm is now investing heavily into the business, Dansky said. It has added 30 employees to the 100 that came over from Sequenom, and will continue to be "in a building mode with [Telegraph Hill Partners'] investment behind us," he said.
Some of that investment is in sales and marketing to support the new approaches. "We're launching quite a few new products, such as the 24-well system, so that's creating some new opportunities to focus on different types of labs," Dansky said. "We're much more focused on the clinical laboratory customer than the previous business was," he said.
MassArray was previously only available in 96-well and 384-well formats, which require upfront automation for dispensing. The high-throughput formats continue to be useful in certain contexts, but, "particularly in the clinical space, smaller labs [and] regional hospital labs ... that are developing their own LDTs have a certain throughput requirement, so we've developed a system that will allow us to get into even smaller labs that don't have the need for so many samples and certainly don't have the funds or necessarily the infrastructure to support a high-throughput platform from us, or even a next-generation sequencing system," Dansky said.
The new 24-well system "fits into a broader set of potential laboratories with the same applications, data performance, and all the same flexibility of our [larger format] system," he said.
The different formats are also upgradeable and downgradable, Dansky noted. The core mass spec instrument itself remains the same in the smaller format, but larger and more widely spaced wells enable manual dispensing, which in turn reduces costs.
The US list price for the 24-well format is $141,000. The cost of consumables depends on the number of markers, but can be as low as $10 per test.
Agena is now developing strategies to market MassArray as a complement to next-generation sequencing and as a diagnostics development tool.
For example, MassArray can be used for orthogonal validation of results, whether validating the workflow process or validating putative hits on a sequencer, Dansky noted.
Agena has also developed an application that can be used in NGS approaches to assay the quality and quantity of DNA from biorepositories, which could be an improvement over current methods given that pre-PCR processing steps can cause experimental variability, he said.
The firm currently markets SampleID, a MassArray method to fingerprint a sample, quantify DNA, and also assesses degree of degradation. There are no publications on the method yet, but Dansky said Agena is working with researchers at the Broad Institute to incorporate the technique into their NGS workflow, and to optimize a new product focused on exome sequencing.
For targeted genotyping, meanwhile, NGS is costly, and "likely overkill," while qPCR- and point mutation-based methods don't allow for much multiplexing.
"From a clinical labs perspective, most of the tests that are relevant in terms of being clinically useful, proven, and reimbursable, fall into a range of tens to a couple hundred markers," Dansky pointed out.
Dansky noted that a key benefit of MassArray is that it enables rapid test development. Assays can be multiplexed to as many as 50 genetic markers per well, use easily obtained unlabeled oligonucleotides, and the design process is automated by accompanying software. "In a day or two a customer can develop their own assay," he said.
Agena is also now considering the next steps in potentially developing a clinical testing menu for the MassArray.
The firm will soon be launching a CE-IVD version of the MassArray platform, Dansky said, adding that "in terms of test menu, I would say we're keeping our eyes open."
Agena also has a platform called ImpactDx, which has been granted 510(k) clearance for two specific genetic tests for thrombophilia.
"The ImpactDx system is the same instrument and technology [as MassArray], but with a special Dx version of the software ... optimized for clinical use, and limited in its ability to run only the two cleared tests," Dansky explained. "In the future we can and will extend the ImpactDx software to accommodate additional tests which may become IVD cleared," he said, but for now, the company is "really sensing the market and engaging with our customers who are developing tests to identify the best content."
The firm has also developed a technology to detect somatic mutations called UltraSeek, which enhances sensitivity of the single-allele base extension reaction, or SABER, method for MassArray genotyping. The chemistry can be multiplexed for up to ten mutations, and suppresses detection of wild-type alleles, allowing for detection of as low as a tenth of a percent allele frequency, Dansky said.
A combination of UltraSeek and the 24-well MassArray may position the platform well as an assay for liquid biopsies in the oncology testing market, he said, particularly in clinical labs processing small numbers of samples for a handful of markers. Genes relevant to companion diagnostics can be "tested very quickly, at low cost and high confidence on the MassArray system, [and] that may resolve more than 50 percent of the cases coming through a lab ... those for which there is not a direct answer are a good candidate for sequencing."
The firm also recently launched new software and a general-purpose kit so that customers can design their own UltraSeek assays.
Agena is currently "very focused on partnerships," Dansky said. "We're engaging with other companies who want to develop content on this platform, and that's likely the first way that IVDs, whether in the US or in other countries, will get developed."