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OGT Focuses on Small NGS Cancer Panels for Clinical Research; Will Launch CE-IVD NIPT Array

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NEW YORK (GenomeWeb) – Oxford Gene Technologies plans to develop a suite of narrowly targeted, disease-specific next-generation sequencing panels for the translational market in cancer and inherited disease, and also is working on an array-based test for noninvasive prenatal screening, company officials told GenomeWeb.

Last week, the Oxfordshire, UK-based molecular genetics firm launched an ovarian cancer panel and a library prep kit that Executive VP of Research and Development John Anson said would be the first of a number of NGS-based panels.

"It is very much a move into a much more targeted area, with specific diseases," Anson told GenomeWeb in an interview.

Last year, the company launched a 60-gene solid tumor panel, which it developed in collaboration with the University of Southampton, the University of Birmingham, and CIS Healthcare as part of the UK's Stratified Medicine Program. While that panel includes genes relevant across a broad range of solid tumors, Anson said the firm is now focusing on smaller, disease-specific panels.

The ovarian cancer panel, for instance, targets just seven genes — BRCA1, BRCA2, TP53, PTEN, ATM, ATR, and NF1. The company plans to develop targeted panels for various solid tumors as well as hematological cancers, and tt already offers a 25-gene myeloid panel. However, in the future, it will develop smaller panels for specific hematological disorders, Anson noted.

He said the company is positioning its NGS panels for translational research customers, like large cancer laboratories in both hospitals and academic institutions, which will use them to identify prognostic markers, markers that inform drug response, and new drug targets.

"We want to link this in a research setting to investigations into new potential therapies," he said.

Anson added that the company would also collaborate with customers on the design of some of its cancer panels to ensure that the relevant genes are included.

The NGS cancer panel market is particularly competitive. The major NGS companies — Illumina and Thermo Fisher Scientific — market cancer panels, as do sample prep companies Agilent and RainDance Technologies, and many major academic institutions run their own panels.

Nonetheless, Anson said that OGT's expertise in bait design would help distinguish it from the competition. "We do empirical optimization of bait design," he said, rather than rely on publicly available software. In addition, the company uses its own software on the back end for data analysis, he said.

While OGT has been known primarily as a microarray company, Anson said, the firm has run over 6,000 NGS samples.

Graham Speight, director of R&D at OGT, said the firm also prides itself on maintaining even coverage across the entire targeted region, which is especially important for detecting somatic mutations, where minor allele frequencies can be below 1 percent or in the ovarian panel. In addition, for tumor suppressor genes, such as those on the ovarian cancer panel, coverage of the entire gene is critical, since mutations can be found throughout the gene as opposed to oncogene where mutations often cluster in hotspot regions. "You need to cover every base of every exon to get the sensitivity that you need," he said.

In addition, Anson said, OGT offers complementary products. Last year, it acquired Cambridge-based Cytocell. Anson said that Cytocell's fluorescence in situ hybridization products, as well as OGT's own cytogenetics arrays, complement its NGS offerings. "There's a nice crossover between using arrays to look at copy number variants and NGS to look at SNVs," Anson said.

While the firm is focusing initially on the clinical and translational research market, and all of its NGS products are marketed as research-use only, Anson said that the company is eyeing the clinical market.

"If these tests are found to be important for diagnostics, we're prepared to go down the regulatory route," Anson said. "It's something we've done with some of our FISH products and something we're anticipating as the regulatory environment moves in that direction."

Anson anticipates that the cancer panels could be narrowed down even further before they were brought through regulatory approval, focusing only on the genes or specific mutations that were found in the pre-clinical work to have relevance for therapy, diagnostics, or prognosis.

Aside from cancer, the firm is developing products in the constitutional disease space and is moving into the noninvasive prenatal screening market.

By the end of the year, OGT plans to submit an NIPT for clinical approval in Europe as a CE-IVD, and expects to launch the test in 2016. Currently, the firm is in the midst of conducting a clinical trial of the test, which will use microarray technology to screen for Down syndrome.

Anson said the firm decided to develop the NIPT on an array platform as opposed to NGS because it has a quicker turnaround time and potentially could be offered at a lower cost. Turnaround time for the microarray NIPT could be easily done within three days, he said. Currently, most NIPT companies offering NGS-based tests claim turnaround times of about seven to 10 days, although UK-based Premaitha Health, which has developed its NGS-based Iona test as a kit, also says turnaround time is three days.

Similar to its other products, OGT will market the NIPT as a kit, rather than a testing service.

OGT also offers an array-based preimplantation genetic screening test, which Anson said would not be converted to NGS in the foreseeable future.

The firm has also focused primarily on array-based products for the constitutional disease space, however, Anson said that NGS-based panels could complement OGT's existing array-based products in this market. Currently, the firm markets a medical research exome array that it designed in conjunction with Emory Genetics Laboratory.

The array contains enhanced coverage of 4,600 genes relative to medical research and grouped into disease- and syndrome-specific panels. OGT designed it to be complementary to exome sequencing and Madhuri Hegde, executive director of EGL, previously told GenomeWeb that OGT's array could accompany EGL's own medical exome test for better detection of deletions and duplications.

OGT also offers focused arrays for a range of other genetic disorders including autism, Duchenne muscular dystrophy, epilepsy, intellectual disorders, hearing loss, metabolic disorders, and more.

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