Caitlin Smith has a B.A. in biology from Reed College, a Ph.D. in neuroscience from Yale University, and completed postdoctoral work at the Vollum Institute.
Molecular-diagnostic tests are used to identify biomarkers associated with particular diseases or conditions, to monitor the effectiveness of drug treatments and most recently to monitor patient care. Advances in sampling technology and data analysis are helping make molecular diagnostics more acceptable to clinicians and more easily adopted into their workflow. Here’s a glimpse at how molecular-diagnostics assays and tools are evolving based on research needs.
Noninvasive samples
The trend to studies using noninvasive materials, such as blood or urine, continues to evolve, to the benefit of patients (who are not subjected to invasive or surgical processes to remove tissue samples) as well as clinicians. “One very active area of oncology research is the molecular interrogation of circulating tumor cells (CTCs) and cell-free DNA from blood to obtain real-time information from each patient,” says Mike Nolan, vice president and general manager of oncology at Thermo Fisher Scientific. “These approaches could open the door to new types of molecular-diagnostic tools to further inform care decisions.”
Affymetrix’s CytoScan Dx Assay, which uses blood samples to perform whole-genome microarray analysis, was recently cleared by the U.S. Food and Drug Administration (FDA) as an aid in diagnosis for children with developmental delays or intellectual disabilities. Affymetrix’s OncoScan FFPE Assay Kit, a for-research-use-only assay, has been used in studies to characterize copy number alterations in circulating cell-free (cf)DNA, says Guy Afseth, Affymetrix’s director of marketing, clinical applications. In the Powered by Affymetrix program, the company has partnered with Ariosa Diagnostics in supplying arrays for Ariosa’s noninvasive prenatal-testing Harmony assay, which evaluates circulating fetal DNA from maternal blood samples.
Smaller samples
Samples for molecular-diagnostics tests are also becoming smaller, by design of the instrumentation. One example is HTG Molecular Diagnostics’ HTG EdgeSeq system, a next-generation sequencing (NGS) based automated system that prepares samples and then integrates with NGS instruments for detection and quantitation.
“A major unmet need in the market is being able to utilize samples without a lot of pre-analytical steps, [such as] RNA extraction, reverse transcription and purification steps,” says TJ Johnson, CEO of HTG Molecular Diagnostics. As a result, precious samples, such as rare formalin-fixed paraffin-embedded (FFPE) tissues, aren’t used up as quickly. “As biopsies become less invasive, people are moving away from surgical resections and more into [smaller] core needle biopsies,” Johnson says, making it all the more important “to be able to do this type of highly multiplexed molecular profiling from … increasingly smaller samples,” he says.
Nolan agrees that with more potential biomarkers comes an increased need for multiplexed testing. “This is especially true in oncology, where small biopsies and fine-needle aspirates are common,” he says. “Using traditional approaches of sequential testing, there is a significant risk that the sample could be consumed before meaningful information is obtained.” This is fostering a shift toward a targeted NGS approach for molecular interrogation. Tools in this arena include Thermo Fisher Scientific’s CE-IVD Oncomine Solid Tumour DNA kit, an NGS oncology assay based on the Ion Torrent AmpliSeq technology, which enables detection of single-nucleotide variants, insertions and deletions using as little as 10 ng of FFPE DNA. Similarly, the CE-IVD Oncomine Solid Tumour Fusion Transcript kit enables detection of rearrangements involving the ALK, ROS-1, RET and NTRK1 genes by RNA sequencing.
Affymetrix’s new GeneChip WT Pico Kit is designed to target prepare very small amounts of sample RNA. “There’s a huge amount of interest in looking at smaller and smaller subsets of cells, particularly in cancer research because a lot of tumors are made up from a heterogeneous population of cells,” says Mindy Lee-Olsen, vice president of marketing services at Affymetrix. “Scientists are very interested in looking at specific subsets of cells.” The WT Pico Kit lets researchers prepare RNA from as little as 100 picograms of total RNA, or as few as 10 cells for a whole-transcriptome analysis on expression microarrays.
Creating actionable results
A hallmark of a good test is that it provides actionable data—that is, based on the test outcome, both doctors and patients know what set of actions will come next. SCIEX’s GenomeLab GeXP™ Genetic Analysis System, a capillary electrophoresis instrument that estimates fragment sizes of DNA labeled with fluorescent dyes, is intended for general clinical use. “[It] can measure a variety of analytes as an aid in the diagnosis and treatment of various disorders or conditions,” says Handy Yowanto, global senior product manager at SCIEX.
With less-specific tests, such as whole-transcriptome arrays, clear, actionable answers don’t typically emerge from the instrument into the clinic. “One of the biggest challenges is the availability of skilled clinicians or medical doctors who are trained in deciphering genetic data into clinically relevant information, to meet molecular testing industry growth demands,” says Yowanto. In addition to training, instrumentation, informatics and software are likely to integrate and adapt to make molecular diagnostics easier to read and use. “The more information the better, but you have to overlay that with the fact that the information has to mean something, that it has to be actionable,” says Afseth. “In the clinic, especially, people don’t want to get information unless they can act on it.”
Indeed, Johnson agrees that a major challenge is interrogating data for actionable results. “Because at the end of the day, clinicians don't want to look at a whole-genome profile,” he says. “They want to know what's actionable to them based on the therapies they have available.”
Going forward
In the near future, molecular diagnostics is likely to undergo some developments that will lead to greater adoption in the clinic. The first of these will be the increased use, and mandate by the FDA, of companion diagnostics. “If you consider the current drug pipelines, especially in oncology, a significant number of new therapies are likely to require a companion diagnostic, which will further accelerate the use of molecular information in treatment decisions,” says Nolan.
The second improvement will be the simplification of the workflow to allow a “decentralization or democratization of molecular diagnostics,” Johnson says, adding that while roughly 500 labs can do high-end molecular profiling, 10,000 labs see patients. He predicts that within the next 10 years, today’s “high-end testing” will be adapted for use in many smaller community labs.
The fast pace of such change—and the use of smaller, noninvasive samples—is helping to move molecular diagnostics forward into the clinic, expanding its diagnostic role into prognosis and treatment. Future progress will be facilitated by developing more actionable readouts for clinicians. Keep an eye on molecular diagnostics, as it’s about to become a workhorse in the clinic.