Paragon Applies Amplicon Panels for Targeted Sequencing To COVID-19

By Allison Proffitt

June 24, 2020 | A key question for life sciences companies in the past few months has been how dramatically to respond to the COVID-19 pandemic. How much of the company’s existing work should be shifted or put on hold for efforts to diagnose, treat, and monitor our most pressing health issue?

Paragon Genomics, based in Hayward, Calif., began watching the situation in January, Tao Chen tells Bio-IT World. “Back in January, we’d been monitoring the China COVID-19 situation very closely, realizing that a pandemic could be spreading to other countries like the US. We definitely kept a close eye on the situation.”

Paragon Genomics provides amplicon-based target enrichment technology for targeted sequencing. The company’s CleanPlex NGS panels feature a multiplex PCR primer design algorithm, uniform multiplex PCR amplification chemistry, and patented background cleaning chemistry. Amplicon sequencing is faster, less complicated, and more sensitive than hybrid capture-based sequencing, Chen argues, so CleanPlex technology lets users reach their targets with much lower DNA input, thus saving time and cost. Panels run on Illumina and MGI sequencing systems; Ion Torrent is being tested. And CleanPlex panels are being used by over 200 customers; Chen mentions the Mayo Clinic, Stanford University, UCSF, and SOPHiA GENETICS.

Paragon offers ready-to-use amplicon panels for a host of applications including BRCA 1 and BRCA 2 panels, hereditary cancer panels, tumor mutation burden panels, lung cancer panels, non-invasive prenatal testing and more. But the majority of Paragon’s business—60%-70%—is in custom panels.

Customers come to Paragon with a list of genes or mutations they want to explore, and the Paragon design team uses proprietary software, Paragon Designer, to design PCR primers targeting loci or regions of interest. The Paragon Designer software designs the primers while minimizing primer dimers and nonspecific PCR products, Chen says. “After design, we’ll report back to the customer telling them the coverage and the in silico performance of the panel. If the customer is satisfied with the report, they’ll place an order with us,” Chen says. The primers are delivered to the customer with the target library prep kit. “Now they can perform target sequencing in their own labs instead of sending their samples to some core lab or some other specialized testing labs,” Chen says.

COVID-19 Panel Launch

As COVID-19 spread worldwide, it was clear that a SARS-CoV-2 panel was needed.

“In March, we saw the need to actually create something for this. Within a month we were able to come up with a ready-to-use COVID-19 full genome sequencing panel using our CleanPlex technology,” Chen says. “We designed about 340 amplicons covering the full genome of the SARS-CoV-2 virus. Because we are using an amplicon-based method, it’s very sensitive. We can detect down to just a few copies—one or two copies—as opposed to some of the capture-based methods.”

Other methods have to sequence a lot, Chen says: 10 million reads to detect 100 copies. The CleanPlex methods needs only 50,000 to 100,000 reads. “It’s like 99% reduction in the sequencing cost to get the full genome information of the virus.”

Paragon launched the SARS-CoV-2 NGS panel on March 19. Since then, Chen says, customers in the US, Italy, Portugal, Germany, and China have been using it. Sequencing platforms are distributing the assay, he said. On March 26, Paragon and SOPHiA GENETICS extended their partnership so that the Paragon SARS-CoV-2 NGS panel would be delivered to SOPHiA’s install base of more than 1,000 hospitals.

The NGS panel is intended for research, Chen says, though he is hearing from customers who see the value of sequencing in virus detection. “Some of the hospital customers are validating our sequencing panel for LDT purposes,” he said.

Next Steps

Creating the single panel won’t be the end of Paragon’s virus-fighting efforts. In the near term, Chen says, the company will have a COVID-19 focus. There are more products in development that Chen expects to release in the next two-three months. “We reason that COVID-19 might come back for a winter season, with the flu season. That will require a different panel to assess both COVID-19 and the flu,” he says.

Even before COVID-19 the company was growing quickly, Chen says. Paragon raised its $8 million Series A round in 2017 and has been funding itself since then. In the past few years Paragon has been doubling sales and revenue every year. “We see ourselves, really, as the partner of choice for NGS panels.”