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Personal Genome Diagnostics Looking to Develop IVD Assays With Pharma Partners

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NEW YORK (GenomeWeb) – Personal Genome Diagnostics is moving forward with a strategy to bring oncology assays through regulatory clearances by collaborating and codeveloping tests with pharmaceutical companies that it will then launch as in vitro diagnostic tests that can be run in laboratories throughout the US and elsewhere.

Recently, the firm discussed initial results of a pilot study with Takeda for a liquid biopsy assay in 12 patients with small-cell lung cancer. Antony Newton, PGDx's chief commercial officer, told GenomeWeb that the firm is now working with Takeda to custom design its assay and validate it in larger patient cohorts, and said that it would eventually bring it through regulatory approvals to launch as an IVD.

The collaboration with Takeda exemplifies PGDx's overall strategy for developing oncology diagnostic assays. PGDx CEO Doug Ward told GenomeWeb that PGDx is currently collaborating with many of the top pharmaceutical companies and is in various stages of product development with different pharma companies — first developing research-use-only assays, then customizing the assay based on the pharma company's specific needs, running the necessary trials with contract research organizations to give it the investigational-use label, and then bringing it through clinical validation and regulatory clearances in the US, Europe, and elsewhere to launch as an IVD. "We're working in all those stages," Ward said.

Over the last year, the company has increasingly shifted from a research focus — developing technology that originated at Johns Hopkins University — to a more commercial focus. It raised $21.4 million in a Series A financing round last year, earlier this year appointed Ward as CEO, and last month struck up an agreement with Illumina to develop IVDs.

The company has three major business segments. It develops research-use-only assays, offers clinical testing services, and has a business segment it previously called Enterprise Solutions but has since rebranded as Progeneus to export its protocols and technology to other labs. It is under this arm that it conducts its collaborations with pharmaceutical companies.

Its research products include 88-gene and 203-gene tumor tissue-based targeted panels, as well as a cancer exome test and a test that combines exome sequencing with HLA typing to identify mutation-derived neoantigens. It also offers liquid biopsy products — a 63-gene panel and a test for detecting MET amplifications.

For its clinical services arm, PGDx offers both the 88-gene and 203-gene tumor tissue tests and the exome sequencing service. And it plans to soon offer the 63-gene ctDNA assay as a clinical service.

Under its Progeneus arm, both PGDx's tissue-based and plasma-based assays are available. The offering includes the firm's proprietary capture probe technology and bioinformatics software as well as the training to laboratories to be able to run the tests with a one- to two-week turnaround time.

Increasingly, PGDx's strategy is to partner with pharmaceutical companies under its Progeneus business segment. In its proof-of-principal study with Takeda, researchers assessed PGDx's 63-gene plasma-based assay PlasmaSelect in 12 patients — running the assay on both circulating tumor DNA as well as DNA extracted from circulating tumor cells. The companies demonstrated that the two techniques were concordant and also concordant with analysis of DNA from the tumor itself. Now, the companies are moving forward with a larger study and with an assay that PGDx has custom designed for Takeda specifically for small-cell lung cancer.

Although PGDx analyzed both ctDNA and DNA from CTCs in that study, the company is not developing technology specific for analyzing CTCs. Instead, Takeda used the CellSearch technology to isolate CTCs and then PGDx ran its PlasmaSelect assay on the extracted DNA.

Theresa Zhang, PGDx's vice president of research services, said that Takeda wanted to analyze both ctDNA and DNA from CTCs to compare the approaches. "One of the major questions that Takeda and others have is whether to use ctDNA or CTCs in order to genotype a patient with a noninvasive assay," she said. In the initial proof of principal, "we showed that in terms of the mutations identified, the two DNA sources are fairly consistent," she said.

Nevertheless, Newton added that although ultimately PGDx's technology was agnostic in terms of whether it would be run on ctDNA or DNA from CTCs, the firm would proceed with ctDNA assay development. "Free DNA is typically more abundant than tumor cells," he said.

Since this initial proof-of-principal trial, PGDx and Takeda have moved ahead with assay development. "This first project was to evaluate the utility of the assay," Newton said. PGDx has now custom designed an assay for Takeda specific to small-cell lung cancer and tested it in a larger cohort of patients, Zhang said. The results of that study have not yet been published, she said.

The next step if Takeda chooses to go that route would be to do a pivotal study of the assay alongside a drug trial. Ward said in that case PGDx would develop the product under quality and design controls that meet the FDA's safety and efficacy requirements for investigational use products and transfer that to a CRO, which would run the clinical trial with the pharmaceutical company.

The goal is then to bring that test through FDA approval so that PGDx can sell the protocols for running it to other molecular diagnostic labs through its Progeneus platform, Ward said.

Ward declined to provide a timeline for when its first products would be FDA cleared or for what indications or what testing methods they would use, but said the firm would provide additional details about the tests in early 2017.

He said that the company planned to also bring its tests through regulatory clearances in Europe and other countries, but was pursuing FDA clearance first. "Our strategy is to meet the bar of the FDA," he said, which should put the company in a good position to meet "most of the regulatory requirements globally." 

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