Molecular diagnostic testing: A healthy prognosis

Caren B. Les, caren.les@photonics.com

Molecular diagnostics is the fastest growing segment of the in vitro diagnostics market, according to a study by DeciBio, a Los Angeles-based market analysis firm. Stéphane Budel, a partner in the company, said the market size, estimated at $4.8 billion in 2010, has experienced a growth rate of approximately 15 percent over the past few years, driven by the increased availability of tests, the rising incidence of chronic diseases related to the aging population, and pharmacogenomics/personalized medicine.

DeciBio published its report Molecular Dx: Market Segmentation and Opportunities in October 2010.

“The market for photonics-based molecular diagnostic tools has been attractive and will remain so in the foreseeable future,” Budel said. The vast majority of molecular diagnostic tests rely on detection of nucleic acids and use some form of photonics-based tool, primarily fluorescence, for sequencing and real-time polymerase chain reaction (PCR), chemiluminescence for transcription-mediated amplification, or a chromogenic method such as in situ hybridization.

The LightCyler, an instrument for rapid online PCR-based applications, is undergoing tests.

In addition, a number of new automated photonics-based platforms, including the San Diego-based Gen-Probe Inc.’s Tigris DTS direct-tube sampling system, have supported the growth and adoption of legacy tests, he said.

Molecular diagnostic tests identify biological markers in the form of nucleic acids such as DNA or RNA. These nucleic acids can be genetic material of foreign organisms, as in the case of an HIV infection, or markers that distinguish normal from abnormal tissue, such as in the case of overexpression of the breast cancer receptor Her-2.

Molecular diagnostic tests do not include microbiology ones that detect whole organisms by culturing them in a dish or immunochemistry tests that detect protein, typically using antibodies.

“Current technologies are well understood, but establishing growth figures for rising photonics-based molecular diagnostics test markets, such as next-generation sequencing or bead-based multiplex technologies, can be difficult, as current utilization is small, making current market size hard to estimate,” Budel said. “Moreover, key customers are still gauging their forecasted level of adoption for the next few years.”

He estimated the real-time PCR market at $2 billion, the transcription-mediated amplification market at $1 billion, the combined in situ hybridization and fluorescence in situ hybridization (FISH) market at $700 million and the sequencing market at $200 million.

“Each of these technologies depends on an instrument with photonics-based elements,” he said. “The key trends affecting these instruments are increased automation, work-flow simplification and multiplexing.

“Multiplexing – the ability to look at multiple analytes in a single sample – is of particular relevance to photonics-based tools, as it depends on the availability of instruments with the right set of excitation sources and filters as well as the existence of appropriate dyes.

“Currently, growth in the molecular diagnostics test market is driven in large part by adoption of multiplex tests because these assays tend to be more comprehensive, only require smaller sample volumes and can eliminate intrasample variability. Advances in personalized medicine necessitate the analysis of multiple analytes in a single sample in order to make a diagnosis; for example, the Oncotype DX from Genomic Health Inc. of Redwood City, Calif., examines the activity of 12 genes in a patient’s tumor. Limiting factors in multiplexing technologies are often linked to cross-reactivity, higher costs and spectral differentiation for signal detection.”

Budel cited four photonics-based molecular diagnostic tools that have gained traction or that are on the horizon: point-of-care readers, next-generation sequencing platforms, low-density bead-based microarray readers and digital anatomical pathology instruments.

Although current point-of-care readers rely primarily on simple tests often based on chemistry/immunochemistry, some companies are beginning to develop molecular diagnostics-based tests because of their higher sensitivity and specificity.

“This evolution is motivated by the increased number of genetic biomarkers found each year and rendered possible by the development and uptake of molecular diagnostic test techniques that do not require thermal cycling, thereby facilitating instrument development,” Budel said. “Some of the key applications for point-of-care readers include infectious-disease testing in the field, such as for HIV, or in hospitals, such as for MRSA [Methicillin-resistant Staphylococcus aureus] infection, where an immediate response is critical for patient triage. The key challenge for these readers is photonics miniaturization.”

Next-generation sequencing platforms enable an entire human genome or transcriptome to be sequenced in about a week for a few thousand dollars, he added. It is starting to be used in clinical settings, in centers of excellence and by companies such as GeneDx Inc. of Gaithersburg, Md. The technology seems poised to revolutionize health care and affect a broad range of stakeholders, with the $1000 genome right around the corner, Budel said.

“These sequencing instruments promise to be a key platform for optics in the next few years,” he added. “One of their key applications will be repeat sequencing of patient tumors to identify mutations in cancer cells that create resistance to drug treatment. The main challenges for this technology are higher sensitivity and resolution of signal from higher picture density.”

Low-density bead-based microarrays also are expected to play an increasingly important role in molecular diagnostic testing.

“These laser-based instruments can measure 50 to 500 analytes in a single sample at a throughput appropriate for clinical settings – especially for hospital-based laboratories,” Budel said. This technology promises to have applications ranging from genetic mutation panels to respiratory viral panels such as flu strains and other viruses. The challenges for bead-based microarrays are higher sensitivity and discrimination of spectral overlaps.

“Digital anatomical pathology may be the future of histology,” Budel noted, and it is used in less than 10 percent of US hospitals and clinical labs. “The technology allows health care providers to digitally capture, store and share images of biopsies from patient tissues on slides. Software can perform some of the work done by a pathologist and help with data interpretation and reflex testing. The key hurdles for this technology are clearer pictures with a 3-D feeling, faster image acquisition and downstream analysis.”

An employee of Roche, based in Basel, Switzerland, works on the production of PCR (Master Mix) reagents for diagnosing the hepatitis C virus. The balance control panel is shown in the background. Images courtesy of Roche.

Roche, Abbott Molecular, Siemens and Qiagen are the major PCR/real-time PCR companies, Budel said. Applied Biosystems and Roche offer two of the most popular laser-based instruments to perform these tests in clinical settings, he said, adding that Gen-Probe offers large-volume tests used for blood screening based on transcription-mediated amplification and hybrid capture technology, while Dako, Vysis (Abbott Molecular) and Ventana Medical Systems (Roche) are key developers of in situ hybridization and FISH.

“Within the latest instrument-based technology, Illumina, Life Technologies and Roche (454 Life Sciences) are top sequencing companies,” he said. “For bead-based technologies, Luminex is the current company of choice. Key digital anatomical pathology suppliers include Roche (BioImagene) and Aperio.”