NEW YORK (GenomeWeb) -- Quest Diagnostics has launched a next-generation sequencing-based 34-gene panel called OncoVantage and plans to collaborate with Memorial Sloan-Kettering Cancer Center for clinical annotation of the test, Quest said this week.
In addition, Quest will collaborate with Memorial Sloan-Kettering to develop a larger panel that will likely include hundreds of cancer-related genes.
The OncoVantage test runs on Life Technologies' Ion Torrent PGM and uses an in-house developed amplicon-based enrichment strategy to generate more than 200 amplicons from the 34 target genes. It has a list price of $2,400 to $2,800 and a turnaround time of 10 to 14 days, Quest's Senior Vice President of Medical, Science and Innovation Jay Wohlgemuth told Clinical Sequencing News.
The test will be able to detect variants down to a 5 percent allele frequency and will require bases be covered by at least 300 reads to call as a mutation.
Beginning this summer, the clinical report that is provided to the ordering physician will include expertise from the Memorial Sloan-Kettering team. Wohlgemuth said that although Quest has been working with next-generation sequencing technology for several years from all the major vendors and has expertise with the technology, partnering with MSKCC for interpretation and annotation will add necessary clinical expertise.
"There are a lot of public domain sources of information, but having a relationship with Memorial where their experts and databases are used to help us get the most up-to-date interpretation around drugs that target the mutations, or clinical trials that are enrolling which might be able to treat a mutation in a cancer we find, that's incredibly valuable to us," Wohlgemuth said.
In return, Quest will contribute de-identified data that it gathers from the OncoVantage test to Memorial Sloan-Kettering's database.
For its initial cancer test, Wohlgemuth said Quest wanted to focus on genes and mutations that are clinically actionable, including those that are in the National Comprehensive Cancer Network guidelines, as well as those for which there is clinical trial data suggesting they are actionable.
Quest is offering the OncoVantage test as a laboratory-developed test, said Wohlgemuth, and does not have plans to bring it through US Food and Drug Administration clearance.
In the first half of 2015, Quest plans to launch a larger panel that will have a list price of around $4,000. Quest will seek expertise from MSKCC in its development. MSKCC already offers a 341-gene cancer panel for solid tumors to a subset of its patients, Michael Berger, a researcher in MSKCC's department of pathology told CSN. That test runs on the Illumina HiSeq.
Berger said that MSKCC would help Quest develop its larger gene panel, and while the Quest panel will likely include the same gene content as MSKCC's panel, Quest will not simply export the test from the MSKCC lab to its own lab, Berger said.
"We'll develop independently the underlying technology to measure the genes, but we do plan to align [MSKCC's] vision with content regarding which genes and exons we'll be sequencing," Wohlgemuth added. The expanded test will launch in the first half of 2015.
With both focused and broader tests, Quest aims to serve the community oncology market as well as cancer centers, pharmaceutical companies, and other larger institutions with more genomics expertise.
"In [the community oncology] setting, to provide a 300-gene panel, for example, might provide much more information than oncologists want or are willing to entertain," Wohlgemuth said, adding that the OncoVantage test will be geared primarily toward community oncologists.
In addition, the clinical report is a vitally important piece in the community oncology world, which MSKCC will help Quest develop. "We're trying to bring what MSK does on interpreting results on cancer to the community oncologist," Wohlgemuth said. "By generating clear clinical guidelines, interpretations, and enhanced reports, we think [broad genomic testing] will be more and more accessible for a community oncologist."
Nevertheless, there is still a substantial market for larger panels that includes cancer centers, pharmaceutical companies, and other markets in which there is "more acceptance and utility in having the much broader information," Wohlgemuth said.
When it launches its expanded panel, Quest will likely compete with Foundation Medicine's FoundationOne test, which currently analyzes over 200 genes but will be expanded to include over 300 genes and 30 gene fusions this year. Foundation has not disclosed the list price of its test, but has reported average reimbursement of $3,400 per test.
In the first quarter of 2014, Foundation Medicine reported receiving orders for 4,702 tests, and the company said that test orders continue to grow. Nevertheless, Wohlgemuth said that he believes Quest is well-positioned in the market, particularly with the agreement with MSKCC.
"We are connected to so many of the docs that need to be using this genomic approach in cancer," he said. In addition, he said the deal with MSKCC will give Quest access to clinical oncologists, clinical interpretation, and actionable information, which will give the company an edge. "Particularly as the market moves toward the use of this in a more commonplace way in community oncology practices and centers, we don't see any sustainable competitive advantage that Foundation Medicine has over Quest," he said.
Wohlgemuth declined to say what platform the expanded assay would run on. Quest has invested in all the major sequencing platforms and has agreements with both Life Tech and Illumina to use their respective sequencing technologies for clinical testing. He said that while the OncoVantage panel would run on the Life Tech platform, subsequent tests could run on different platforms. "We intend to evaluate platforms based on the specific test we're rolling out," Wohlgemuth said.
Quest currently has next-gen sequencing tests in a number of different areas. OncoVantage assesses somatic mutations in solid tumors, but it also offers a BRCA test that analyzes germline mutations, an HIV tropism test, and is developing tests in the areas of neurology and infectious disease, Wohlgemuth said.
The various sequencing technologies have different strengths and weaknesses with regards to read length, error rates, and performance in the various genomic regions of interest, he said. In addition, "a highly important aspect is the software and the flexibility of the software that comes with the system to allow us to generate the data we need for our reports," he said. Each system has differences when it comes to the software, software tools, and their flexibility, Wohlgemuth, so that component is looked at closely with regards to the specific test as well.