This story was originally published June 22.
Molecular diagnostic company Predictive Biosciences last week launched a sequencing-based version of its noninvasive CertNDx bladder cancer assay, in a first step toward developing a suite of sequencing-based tests, including a whole-genome sequencing-based test for prostate cancer.
The company's Cleveland-based CLIA certified laboratory is equipped with four of Life Technologies' Ion Torrent PGM machines, and its Lexington, Mass.-based research lab has an additional PGM as well as Roche's 454 GS Junior.
The CertNDx assay is composed of four different molecular markers of bladder cancer: mutations to the FGFR3 gene, methylation status of NID2 and TWIST1, and the presence of the MMP-2 protein.
Sequencing will only be incorporated into one aspect of the test — determining the mutation status of nine different hotspots in the FGFR3 gene. Currently, quantitative PCR is used to evaluate the gene.
Tony Schuber, Predictive Biosciences' chief technology officer, told Clinical Sequencing News that the company is switching from qPCR to sequencing so that it can detect FGFR3 mutations that are present at below a 1 percent frequency.
Because the assay uses a urine sample as opposed to a tumor biopsy, the majority of the DNA extracted is normal DNA, not tumor, he explained. Currently, qPCR can detect mutations in DNA from a urine sample that are present at around 1 percent frequency, but mutations are often present at a much lower frequency, said Schuber. Converting to next-gen sequencing, the assay will now be able to detect FGFR3 mutations as low as 0.02 percent frequency.
Schuber said the company recently completed a study that will be published soon in a peer-reviewed journal comparing the qPCR version with the sequencing version of the test. The sequencing-based test was able to identify FGFR3 mutations in 30 percent of patients that were deemed negative by qPCR because the mutations were present at a level below the test's threshold of detection.
For the sequencing assay, the company is using amplicon sequencing and will multiplex around 40 samples on the PGM 316 chip. The amplicons will span nine known mutations across three exons. To detect mutations at a 0.02 percent frequency, about 25,000 reads per sample need to be generated, he said.
The test will have a turnaround time of five to seven days. Schuber said payors are currently reimbursing for the qPCR-based test and said that the company will pursue reimbursement for the sequencing-based test.
Given that the test should be more sensitive and less expensive, he anticipates that insurance companies will reimburse for it. He declined to disclose the cost of the test, but said that it would be "much less expensive" than the current test.
A future version of the test will use sequencing for all components — to assess FGFR3 mutations, methylation status of TWIST1 and NID2, and even to determine the presence of the MMD-2 protein, he said.
To use sequencing to detect proteins, he said that the company has developed a technique that makes use of aptamers that bind to the MMD-2 protein. Sequencing can detect the protein-specific aptamer, and the amount of protein can be quantified by "counting how many aptamers are associated with the protein in urine," Schuber said.
He said that the company plans to release the next version of its test, which uses sequencing for all the steps, by the end of the year.
Additionally, Schuber said the company is planning a whole-genome sequencing-based test for prostate cancer. It has not yet decided which platform it will use for this test.
The whole-genome sequencing test will look at chromosome instability in a patient to determine whether the patient has an indolent form of prostate cancer or an aggressive form that may require surgery.
Schuber said Predictive Biosciences holds a patent for "how one can convert events identified in chromosome stability in cancer tissue as an objective result," which he calls a coefficient of instability. Above a certain threshold, a patient is at greater risk for aggressive disease.
While Predictive Biosciencs has launched its CertNDx test as a laboratory-developed test, Schuber said the company is also open to partnerships to take the assay through US Food and Drug Administration approval.
"We are looking to collaborate and partner with somebody to bring it through a kit format, which involves the FDA," he said.