NEW YORK (GenomeWeb) – A team of researchers is developing an assay that analyzes copy number alterations (CNAs) — amplifications or deletions of portions of the genome — to detect tumor growth and metastatic risk in prostate cancer.
Importantly, the test — which uses a genomic DNA signature called the metastatic potential score (MPS) and analyzes CNAs for specific regions of the genome — will likely be more affordable than broader whole-genome sequencing approaches being used to analyze the aggressiveness of cancers, Harry Ostrer, professor of pathology and pediatrics at Albert Einstein College of Medicine and a developer of the test, said in an interview.
The research group, including Einstein and other centers, is developing a diagnostic platform that could be available with the new assay in about two years and used as a laboratory-developed test for clinical diagnosis in hospitals, Ostrer said.
He and his colleagues recently described the assay's performance on cell lines, a cohort of prostate cancer surgical research samples, and matched punched biopsy samples, in a study published in the Journal of Molecular Diagnostics.
The developers are expanding the test to include analysis of metastatic risk in triple-negative breast cancer and lung adenocarcinoma metastases. In the current study, they used an adaptation of the Thermo Fisher Scientific Eureka Genotyping platform, but they are developing the future test to run on the Thermo Fisher AmpliSeq platform.
Copy number alterations in the DNA of tumors may occur from loss or gains in the structural arrangements of chromosomes, and they fit within a class of genetic alterations called genomic instability. CNAs are different from tumor alterations associated with mutations that are not causal and "aren't so predictive of metastasis," Ostrer said. On the other hand, "genomic instability appears to be causal for metastasis, and therefore identifying events through copy number alterations is predictive of metastasis risk," he said.
To calculate the MPS, Ostrer and his colleagues used NGS to analyze copy number alteration gains or losses. They employed a targeted postligation amplification sequencing approach to interrogate 902 genomic sites associated with 194 genomic regions. The test — which the researchers are calling the next-generation copy number alteration assay — is designed to work with the most advanced commercial sequencing platforms.
"In all, we know of up to 366 genes in which a copy is gained or lost and is going to increase the risk of a cancer's metastasis," Ostrer said.
Prostate cancer is tricky to diagnose. Clinicians find it particularly challenging to determine its aggressiveness or its potential to spread to a distant site. That leads to overtreating, including unnecessary prostate surgeries that can have undesired side effects.
In the US each year, physicians diagnose 220,000 new prostate cancers, and 27,000 men die from the cancer. Accurate diagnosis succeeds in identifying men at risk for metastasis, but prostate cancer still spreads in about 16 percent of cases and the medical condition accounts for about 8 percent of all male cancer-related deaths.
Jason Sheltzer, a fellow at Cold Spring Harbor Laboratory and an author on a separate study that covered the role of copy number alterations in cancer aggressiveness, said in an interview, "There is a crucial need to develop prognostic tools for prostate cancer in particular, a condition that is deadly for many men and also commonly overtreated."
He said that data generated by a number of research groups — including the Ostrer lab at Albert Einstein, Charles Sawyers lab at Memorial Sloan Kettering Cancer Center, and his group at Cold Spring Harbor — have demonstrated that copy number alteration analysis can be used to predict the likelihood that prostate cancer will recur.Â
Advances in high-throughput sequencing technology have made it possible to collect terabytes of data from a single patient's tumor, but "a key challenge going forward is developing a way to extract medically useful information from this sort of cancer genomic analysis," Sheltzer said.Â
"By utilizing a targeted approach, rather than a whole-genome or whole-exome strategy, [the assay being developed by Ostrer and his colleagues] may cost less, require fewer computing resources, and be easier to multiplex," Sheltzer said. "While many previous analyses have relied on whole-genome sequencing assays that would be challenging to apply in a clinical setting, the tool described here seems much more feasible to use."
Ostrer said that he and his colleagues have demonstrated that the new assay can detect CNAs rapidly and accurately, enabling the prescription of aggressive therapy at the time of diagnosis for men with metastasis-prone disease. Further, the assay's results can provide a rationale for active surveillance, and therefore an appropriate level of treatment, for men with indolent disease.
DNA extraction, library preparation, and sequencing reagents cost between $20 and $40 per sample compared to nearly $1,000 per sample for whole-genome sequencing, the developers said.
Further, a large number of samples can be processed at one time. The approach enables use of massively multiplexed assays and processing of thousands of samples in a single run lasting about 36 hours, the developers said.
Because samples evaluated with the new assay require far less data storage than whole-genome sequencing, the approach could be implemented in resource-constrained independent laboratories as well as the larger laboratories, Ostrer said.
In previous work, the researchers had developed the MPS as an indicator of metastatic potential using results from DNA microarrays. They found that the score is highly predictive of not only prostate cancer metastasis but triple-negative breast cancer and lung adenocarcinoma metastases.
In the current investigation, the assay calculated the MPS in 70 prostate cancer surgical research samples with known clinical outcomes, and the results were highly correlated with those of a Thermo Fisher Scientific OncoScan CNV assay, a whole-genome copy number variation test.
Further validation
Ostrer said that the assay's technical reproducibility and accuracy have been verified and the research group is looking to integrate it with an existing sequencing platform for analyzing not only the aggressiveness of tumors, but also the expression of genetic mutations that might be predictive of responses to drugs.
They will then work on validating the platform using comparisons with positive and negative controls, he said. Â
Clinicians already use other prognostic biomarkers in diagnosing and treating prostate cancer including prostate-specific antigen level, the Gleason score, and tumor stage. "It will be important to demonstrate that the MPS described here captures prognostic information that improves upon these established markers," Sheltzer said.Â
Among the genomic technologies that would compete with the new assay, if it is released for clinical use, is Genomic Health's OncoType DX score for prostate and other cancers.
"From this current work, it isn't clear whether the MPS will be a superior classifier," Sheltzer said. "Nonetheless, I think that this work represents an important step toward translating cancer genomics for clinical use in prostate cancer."