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GIS Spinout PathGen Dx to Seek FDA Clearance for Chip-Based Test that Can Detect 70K Pathogens

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SINGAPORE— Just over a year after beginning operations, PathGen Dx is moving forward with the commercialization of an assay for infectious disease testing.

The assay, which combines a single PCR amplification with an approximately 170,000-probe array, can identify some 70,000 viral and bacterial pathogens, including many that cannot be detected using other commercial multiplexed pathogen-detection assays, the company said.

According to co-founder and director Christopher Wong, the two-year-old company has immediate goals of securing venture capital funding, pursuing US Food and Drug Administration clearance for the assay, and addressing an estimated annual market opportunity of about $1.5 billion.

Wong, who is also chief scientific officer of translational technologies at the Genome Institute of Singapore, discussed PathGen Dx's plans for its flagship product, PathChip, during the joint annual meetings of the Human Genome Organization and the International Genetics Federation, held here this week.

He told BioArray News that PathGen Dx recently completed its first year of business, selling its Affymetrix-manufactured chip to GIS, Duke-NUS Graduate Medical School, as well as other customers in the island country. With about $250,000 worth of first year sales, the company is eager to work with distributors to expand overseas, Wong said.

In addition, he said that PathGen Dx is courting venture capital firms to fund clinical trials for an anticipated FDA submission as part of a larger strategy to see PathChip adopted in a number of large countries, particularly in public health laboratories, universities, hospitals, and pathology labs.

"We've done the calculations," Wong said. "If we sell the chip for $450 and concentrate on five countries — Singapore, the US, Canada, the UK, and Germany — based on instances of infectious disease cases reported and hospitalizations, and, being conservative, [we capture] a 1 percent market share, we would be addressing a market of about $1.5 billion," said Wong.

What's more, Wong claims that 28 percent of patients hospitalized with an infectious disease are diagnosed accurately.

According to the company, PathChip may be able to increase those percentages. Wong referred to a study that appeared last month in the Journal of Clinical Microbiology that compared the ability of the PathChip to determine the viral etiology of respiratory tract infections in 290 Filipino children with RTIs versus culture and two other FDA-cleared tests sold by Eragen and Luminex.

The study, which was authored with colleagues at the University of Colorado School of Medicine and other institutions, found that PathChip had "good diagnostic accuracy" ranging from between 85.9 percent for rhinovirus and enteroviruses to 98.6 percent for PIV 2, compared to the other methods. In addition, the researchers claimed that PathChip identified a number of viruses not detected by the other methods.

"The published results showed that the chip performed as well as the FDA-cleared platforms, with the advantage that we can detect a lot more pathogens than those other panels can test for," said Wong.

The firm's assay relies on tagged-random primers designed using an internally developed methodology to amplify a large set of pathogen genomes simultaneously in one PCR reaction. The tagged-random primers can also amplify unknown pathogen genomes, PathGen Dx claims on its website.

Currently, more than 50,000 viruses comprising 59 families and 156 genera can be identified at the species and strain level, as well as more than 20,000 bacteria consisting of 26 genera, the company claims.

The chip also contains additional probes that will reveal where mutations are in the detected pathogen, so that researchers can develop PCR primers for characterizing those mutations in other samples.

It is that "comprehensiveness" that PathGen Dx is attempting to parlay into international commercial success, Wong said. In comparison, he noted that Luminex's Respiratory Virus Panel, or RVP, can detect 18 viruses and subtypes.

Taking It Forward

The roots of PathChip stretch back a decade to when Wong and colleagues at GIS worked to develop an array capable of detecting sudden acute respiratory syndrome or SARS. The same researchers further developed the technology, introducing a Roche NimbleGen-made resequencing microarray that they claimed could be used to identify over 20,000 different pathogens (BAN 6/2/2009).

Wong said he and colleagues decided to move the array to the Affymetrix GeneChip platform in 2011 as they wanted to make it available on an FDA-cleared platform. They initially contacted Affymetrix and Illumina about licensing the chip and commercializing it, "but by that time, we had drawn up business plans and wanted to see what would happen if we took it forward ourselves," Wong said.

The result was PathGen Dx, which, beyond Wong and fellow GIS researchers and cofounders Martin Hibberd and Ken Sung, now includes a chief technology officer, general manager, and laboratory technicians.

"This little company is actually an experiment in itself because at GIS we want to try and have greater medical impact," said Wong. "In the past, we would license things out, but we don't have much control over those things and nothing really has been commercialized to our satisfaction by third parties, so we decided to do things by ourselves and to see where it goes," he said.

Last August, PathGen Dx inked a Powered By Affymetrix agreement with the Santa Clara, Calif.-based vendor, under which Affymetrix agreed to manufacture PathGen Dx's test and distribute it globally (BAN 8/28/2012). The Powered by Affymetrix program also provides PathGen with access to Affy's international distribution network.

However, unlike some other Affy diagnostic partners, Wong said that PathGen Dx has "tweaked" the array vendor's protocol, allowing it to deliver a result in about 24 hours, versus the three days required to process other GeneChip-based assays.

To accomplish that, he said that PathGen Dx changed the concentrations of the reagents used in an Affymetrix GeneChip assay, as well as its hybridization method. The vendor now makes a new "reagent cocktail" for PathGen Dx's use, he said.

While PathGen Dx's test has always been offered using microarray technology, Wong noted that the firm's IP is not platform-specific, and that the chips content could be migrated to other platforms, including point-of-care systems, in the future.

"Right now, we are using an Affymetrix system because the chip cartridge is very well-manufactured and some hospitals already have it," said Wong. "We think that if we get our assay approved, there will be a very low barrier of entry to reaching key hospitals and thought leaders."

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