NEW YORK (GenomeWeb) – This week, Cancer Genetics launched a next-generation sequencing-based targeted panel for chronic lymphocytic leukemia, its first NGS-based test, and is planning additional targeted panels, including ones developed through OncoSpire, the commercial entity it formed in collaboration with the Mayo Clinic last year.
Cancer Genetics CEO Panna Sharma told GenomeWeb this week that the company plans to focus on very targeted panels of actionable mutations, initially in blood-borne cancers. The first panel, Focus::CLL, targets seven actionable markers in seven different genes: TP53, NOTCH1, SF3B1, BIRC3, ATM, MYD88, and CARD11.
"Our focus is to develop targeted clinically actionable content," Sharma said. Large panels of several hundred genes are "ideal for diagnostic odyssey type work," he said, for instance in patients that do not respond to treatment, develop metastatic disease, or in which the diagnosis is unclear. "But when people are symptomatic in oncology and specifically on the blood-borne side, clinicians are asking specific questions." In addition, he said, the larger panels are not always economical and many of the findings are not actionable.
Sharma said that the company chose CLL as its first foray into NGS because of its extensive background in the disease as well as the availability of known clinically actionable markers. In addition, the company had already been running a similar test on a microarray platform.
In CLL, he said, there are three genomic signatures that can be evaluated in order to classify the patient as either high risk, intermediate risk, or low risk. "Overall survival and time to first treatment required are very different" for the different genomic signatures, he said. The seven mutations in the CLL panel will answer that question as well as whether or not the patient will respond to conventional therapy.
The test runs on the Illumina MiSeq platform, although Sharma added that the company is platform agnostic and also has a HiSeq as well as Thermo Fisher's Ion Torrent PGM.
Aside from offering the test to clinicians and healthcare providers, Sharma said that the company is marketing it to pharmaceutical and biotech companies that want to evaluate patients as part of a clinical trial.
Cancer Genetics is also looking to launch additional panels in hematological cancers, including a multiple myeloma panel being developed by OncoSpire and a diffuse large B-cell lymphoma panel. The firm is also developing a renal cancer panel on the MiSeq as well as a cancer hotspot panel assessing 50 genes on the PGM and a pharmacogenomics panel looking at 1,885 polymorphism on the PGM.
Cancer Genetics is also planning a large trial in India to evaluate 100 to 200 patients with the hotspot panel to determine whether it can identify any population-specific variants and potentially tweak the panel for the Indian population if need be. He said that trial would likely start in January.
OncoSpire Genomics
Last year, Cancer Genetics and the Mayo Clinic launched OncoSpire Genomics, a Rochester, Minn.-based commercial entity focused on cancer biomarker discovery.
Sharma said that OncoSpire is initially focusing on three disease areas — multiple myeloma, and lung and follicular cancers. Its first product will be a targeted panel for multiple myeloma that will launch in early 2015 through both Cancer Genetics and the Mayo.
There are several differences between OncoSpire and Cancer Genetics, Sharma said. OncoSpire will be able to leverage the Mayo Clinic's biobank and clinicians. Additionally, the company is more focused on drug target and biomarker discovery, rather than answering specific questions about a patient's disease.
OncoSpire will retain the rights to the druggable targets and "proprietary insights" gained from the discovery work, Sharma said, with the goal of outlicensing it to pharmaceutical companies to for drug development.
At this month's American Society of Hematology meeting in San Francisco, researchers from the Mayo Clinic presented data on the 77-gene panel. According to the abstract, the panel encompasses 1,271 amplicons from 77 genes that are either mutated in MM with an incidence of 3 percent or greater, represent important pathways, are targetable, or are associated with drug resistance.
The group ran the panel on 38 patients, 29 of whom were treatment naïve and 9 with multi-drug refractory disease. They used 20 ng of starting DNA and sequenced to an average depth of 964x.
In 89 percent of patients, the researchers identified at least one mutated gene, and 92 percent of the mutations were predicted to be damaging. KRAS was the most commonly mutated gene in 37 percent of patients, while the MEK-ERK pathway was the most commonly mutated pathway in 61 percent of patients. Overall, the researchers said that the findings frequently included "prognostically significant information, actionable targets, and mutations in genes related to drug resistance." Furthermore, as targeted mutation analysis starts to become part of the clinical workup of MM patients, the panel will be a "suitable tool to provide information needed to guide precision therapy and to set the basis for individually tailored treatment decisions," they concluded.