A group at the University of Oxford has begun offering a sequencing-based cancer test that uses Life Technologies' Ion Torrent PGM — the first sequencing-based product developed under the UK's Stratified Medicine Program.
About a year and a half ago, the UK's Technology Strategy Board provided funding for six tumor-profiling projects, three of which were sequencing-based, with a total of £5.8 million ($9.4 million) under its Stratified Medicine Program.
The three academic/industry projects were led by Life Technologies, Oxford Gene Technologies, and Source BioScience. While the Life Tech/Oxford group is furthest along in development, both OGT and Source plan to launch their tests this year.
The Technology Strategy Board set a number of requirements for the tumor profiling tests, including that they must screen for at least 22 mutations in nine known cancer genes, cost less than £300 ($450), have a clinically relevant turnaround time, and have the capacity to "grow in line with future demands" (CSN 6/21/2012).
While the TSB funded the lead companies in the project, the program also collaborated with Cancer Research UK, which helped "line up academia, industry, and medical [professionals]," Graham Bell, the lead technologist at the TSB, told Clinical Sequencing News.
Working alongside CRUK, the groups all have access to 9,000 patient samples and three "technology hubs," which are based at regional testing centers in Cardiff, Birmingham, and Marsden. The technology hubs are "potentially how the companies will access the market," Bell said.
Oxford, Life Tech
Researchers at the University of Oxford, which collaborated with the Life Tech group, recently completed an 80-patient validation study of their test and are now offering it to patients through the accredited molecular diagnostic laboratory at the university.
The test runs on the PGM and screens for the same 46 genes that are part of Ion's AmpliSeq Cancer panel. Anna Schuh, who heads the molecular diagnostic lab at Oxford, said that the lab is starting with a relatively small number of samples, around 50 patients per month, but plans to scale up and advertise the test more broadly in early 2013. Additionally, it is preparing a 150-gene targeted sequencing test.
While the test assays the same genes that are part of the Ion AmpliSeq panel, Schuh said that the team needed to make a number of adjustments and improvements to the test before implementing it clinically.
"A lot of optimization and development work has gone into this," she said, including work in optimizing the primer mix, the bioinformatics, and quality assurance.
"There's a lot of nitty gritty in getting the primer mix right," she said. Another area they had to do a lot of work in was the bioinformatics, particularly for calling deletions.
"The available software tools basically throw out the reads they can't do anything with," which often includes actual deletions, since read depth is lost across deletions. As such, "important deletions like EGFR are not detected, and 50 percent of lung cancer patients have those deletions," she said.
Schuh described it as a "hotspot plus" test because while it looks at hotspot mutations from the 46 commonly mutated genes it also captures 150 base pairs upstream and downstream of those hotspots and can detect some structural variants like EGFR deletions and MET amplifications that predict resistance to EGFR inhibitors.
In order to validate the test, the team ran it alongside mutation testing using a combination of Sanger sequencing and pyrosequencing, Schuh said, to compare results from 80 patients.
All mutations that were detected with Sanger sequencing and pyrosequencing were also detected on the PGM, Schuh said. Additionally, the PGM picks up more mutations than the other approaches because "we can pick up low-level mutations that we can't with Sanger," Schuh said.
Initially, the test is being offered to patients with lung cancer, colorectal cancer, and melanoma because the laboratory already screens for mutations in these patients using conventional methods and the clinical utility has been proven for these indications.
Additionally, "it turns out to be cheaper than conventional testing," which costs ₤100 to ₤150 ($161 to $242) per mutation, compared to ₤300 ($450) for the 46-gene next-gen test, Schuh said.
In 2013, the lab also plans to launch a 150-gene test, which the Oxford and Life Tech group originally planned under the TSB funding. Schuh said the team opted to start with the 46-gene test because it felt it needed an intermediate step between the three or so genes the lab screened for with Sanger sequencing and a 150-gene next-gen-based panel.
Speaking at the American Society of Human Genetics meeting in San Francisco in November, Jenny Taylor, program director of genomics and pathology at Oxford Biomedical Research Center, said that the 150-gene panel will first be tested retrospectively in 500 patients and then the lab will conduct a 1,000-patient prospective study.
Oxford Gene Technologies
While the Oxford/Life Tech group is the furthest along in the development and implementation of its test, Oxford Gene Technologies, which was also funded by the UK's Technology Strategy Board, plans to finish validating its 50-gene assay in early 2013, James Clough, OGT's vice president of clinical and genomic solutions, told CSN.
The company has been collaborating with the University of Southampton, University of Birmingham, and CIS Healthcare to develop the panel, which it has been running on the Illumina MiSeq platform.
The academic partners are currently testing the panel for reproducibility and assay performance, running the assay on samples with known but blinded genotypes, Clough said. If validation goes well, he said, the panels could be offered to patients routinely as early as the summer of 2013 as a parallel assay to the centers' standard tumor profiling methods.
Aside from offering the panel through the academic partners, Clough said OGT would eventually like to offer a clinical next-gen sequencing service. Under that model, Clough said that the company would be like a "technical processing laboratory." The assay would be run at OGT's labs, but clinical decision making would still be left to oncologists.
OGT's array services are accredited for clinical use, and Clough said the company is now exploring how to offer clinical sequencing services.
He said there are several options for offering clinical sequencing tests, including offering one comprehensive panel for all types of cancers, or splitting the larger panel into smaller ones for specific indications.
The advantage of offering just one panel is that "you treat all samples the same, and it's straightforward," Clough said. However, breaking the panel up into smaller panels geared toward specific indications could make the panel more cost-effective, especially if greater sequencing coverage is needed, he said.
For instance, said Clough, a panel may include a large number of genes, many of which are not of interest. If 1,000-fold coverage is necessary for the genes that are of interest, it "may make sense to do separate panels," he said.
Moving forward, one key question is how these tests will be reimbursed, which will likely influence how they are offered. That infrastructure should become clearer in the UK over the course of 2013, Clough said.
Additionally, he said, more research needs to be done to show that next-gen sequencing tests impact patient outcomes.
"One aspect of this that is important is 'how can we successfully fight cancer in as cost-effective a manner as possible?'" he said.
Source BioScience
The third company to be funded by the TSB to develop a targeted cancer panel, Source BioScience, is aiming to launch its 100-gene test in the second half of 2013.
Currently, the company is "tweaking" its selection kit to optimize performance and make sure that coverage is even, Tom Burr, research and development manager at Source BioScience, told CSN.
Like OGT, it is also developing the test on the MiSeq, and using Agilent's HaloPlex enrichment technology. The company has been collaborating with the Barts Cancer Center.
Burr said that the company is also looking to offer the test as an accredited service.
"We're quite a large provider of molecular diagnostic testing in the UK," Burr said. "It's a very natural step for us to offer this test to our same customers."
The 100 genes on Source BioScience's panel includes both the common targets as well as an "additional set of targets that we believe might be of interest in the future that aren't on existing panels," Burr said.
He did not specify what those targets were but said that they would be targets of interest to researchers developing new therapies, and that the inclusion of these targets would help distinguish the panel from other targeted cancer panels.
Burr said that the company would be looking to market its test to individual clinicians within the UK National Health Services. It would be up to clinicians to decide whether they prescribe the test for newly diagnosed patients or patients with advanced cancer. As specified by the TSB, Burr said the test would cost ₤300 ($450) or less.