NEW YORK (GenomeWeb) – Trace Genomics, a startup that participated in Illumina's accelerator program under its previous name PathoGn, has raised $4 million in seed investment and launched its first service — a panel that tests for 12 soil-born pathogens that cause disease in lettuce and strawberry crops.
The company's Cofounders Diane Wu and Poornima Parameswaran told GenomeWeb that the company is initially targeting growers in California's central valley, but that the test is available to anyone to order. Aside from growers, Wu said that international conglomerates like Coca-Cola that work with farmers to increase productivity may be interested in the firm's testing services.
The company is based in San Francisco and has eight full-time employees, but it is rapidly growing, Wu added.
Trace Genomics' test uses Illumina next-generation sequencing, but the real advances are related to its proprietary technologies around the molecular biology, sample prep, quantitation, and bioinformatics that make it more than just a plug-and-play sequencing test, the cofounders said.
In addition, while the initial offering screens for 12 pathogens that impact strawberries and lettuce, the underlying technology is crop agnostic, and the company plans to expand to a broader array of pathogens and crops as it takes aim at the $4 billion worldwide agricultural testing market.
The test costs $199 and has a turnaround time of two to three weeks.
Currently, most soil testing laboratories rely on culture-based methods and PCR to diagnose pathogens, Parameswaran said. But those tests rely on the ability to culture microbes and many cannot be cultured. They also assume the knowledge of the specific strain and only test for one pathogen at a time, she said.
The advantage of using NGS is the ability to look agnostically and at multiple pathogens at once. However, soil is a challenging substrate to work with, Parameswaran said. "It contains a lot of chemical compounds that inhibit the sequencing." In addition, methods to break apart the cells and extract genetic material are crucial, Wu added.
They declined to disclose details of the technologies they developed for their sample prep methods, but said that they are working with academic collaborators to validate the methods and would publish them in a peer-reviewed journal.
The sequencing component itself is a "blend" of targeted and broad methods, Parameswaran said. While the current readout that is delivered to the customer focuses on the 12 pathogens, Paramaswaran said that the sequencing method itself goes beyond a targeted approach, although she said it was not quite a shotgun sequencing approach either. "One approach won't cut it," Parameswaran said. Wu added that the approach was developed in house and is a "broad umbrella" that enables the firm to detect not only the pathogenic microbes, but also the beneficial ones as well.
Trace Genomics also is continuing to develop its molecular biology techniques, Wu said, and is gearing up to offer a test that would look at the beneficial microbiome.