September 1, 2006 (Vol. 26, No. 15)

As Technology Advances through the Clinical Arena, Costs Are Lowered and Time Is Saved

Biomarkers save money. That simple fact, coupled with a wealth of information to link specific diseases to particular biomarkers, is resulting in explosive growth for molecular diagnostics.

“Molecular diagnostics is proving it can significantly lower the cost and overallLeomics Associates and scientific advisor for CytoCare. Starting patients on the right therapy reduces the trial and error that is a part of modern medicine, resulting in lower toxicity risk and improved outcomes, Dr. Leon explains.

Another advantage of current molecular diagnostics is time saving. “While traditionally, the mere ability to detect otherwise hard-to-measure targets was the key merit of molecular techniques, now the speed factor is gaining more and more importance,” notes Peter Kaspar, Ph.D., corporate vp and head of molecular biology business unit, bioMerieux ( “This can eventually lead to a paradigm shift in patient management, as seen in the use of MRSA screening for admission of new patients to the hospital.”

Multiple Approaches

Much of the interest with using molecular diagnostics is in oncology and genetic testing. The range of options that various companies are exploring includes determining disease risk, genetic screening, diagnostic and prognostic tests, therapeutic selection, monitoring therapeutic response, and monitoring disease progression.

Genzyme ( plans to develop microarrays to diagnose mental retardation and birth defects, according to Robert Wassman, M.D., vp and national medical director. It also is moving toward sequencing tests for cystic fibrosis and lysosomal storage disorders that may let physicians correlate phenotype to genotype and determine therapeutic approaches.

In May, Genzyme introduced two assays for acute myelogenous leukemia (AML): the FLT3 Mutation Analysis and the WT1 RQ-PCR. FLT3 receptor mutations are present in about 30% of AML patients and indicate a poor prognosis. The WT1 RQ-PCR assay is an early-warning system for relapse. By testing for minimal residual disease, it can identify patients at high risk of relapse, weeks to months before a relapse occurs. Before that, in February, Genzyme launched the BCR-ABL Mutation Analysis to monitor patients on Gleevec®. After a successful Gleevec treatment, 4% to 5% of patients develop resistance to the drug, Dr. Wassman explains. This test analyzes secondary BCR-ABL mutations, the most commonly reported mechanism of acquired resistance to Gleevec.

To monitor response to tyrosine kinase inhibitor for non-small-cell-lung cancer, two predictive tests have been launched. One detects epidermal growth factor receptor (EGFR) mutations to a patient’s response to Tarceva® and IRESSA®. The second is based on fluorescence in situ hybridization (FISH) and detects over-amplification of the EGFR gene. For chronic myeloproliferative disorders, Dr. Wassman says her assay detects a mutation in the Janus kinase 2 (JAK2) gene.

Genzyme also is marketing Invader® UGT1A1 Molecular Assay, developed by Third Wave Molecular Diagnostics(, to identify colorectal cancer patients who may be at increased risk for severe adverse reactions to the chemotherapy Camptosar®. Patients with variations in the UGT1A1 gene may have a ninefold higher risk of experiencing decreased white blood cell counts as the result of taking Camptosar® than patients without.


Third Wave expects to present its HPV analyte-specific reagent to the FDA next year. This reagent directly detects the virus that causes approximately 99% of cervical cancers. The as-yet-unnamed assay could get rid of the need for annual tests as it looks for high-risk strains of HPV, which take five to seven years to develop into cervical disease.

The first iteration of this test is a high-risk screen that gives positive or negative results for those 14 strains. Later, a genotyping product will focus on strains 16 and 18, which together cause 75% of cervical cancers. “Enrollment for Phase I trials began in August,” Dr. Conroy says.

The global market, according to Kevin Conroy, CEO at Third Wave, is $150 to $200 million annually, with a 30% to 35% growth rate. This test, he says, will compete head-on with PAP smears, which are 50% to 70% accurate. Before the HPV test, by year’s end, Third Wave expects to launch an ASR format test for adverse reactions to warfarin, called the Coumarin™ dosing test. It is available currently for research use and benefits from a recent FDA decision to re-label Coumarin. The issue, Dr. Conroy elaborates, is that the rate at which patients metabolize Coumarin varies widely, resulting in 10-fold variations in dosages. Getting the dosage right typically takes four to six attempts. Consequently, “it accounts for the seventh largest cause of admissions to hospitals and clinics.”

PSA Challenge

Gen-Probe ( is developing a molecular urine test for PCA3, a highly specific prostate cancer gene. The test, explains Harry Rittenhouse, Ph.D., senior director of cancer research, detects elevated levels of PCA3 mRNA and may help reduce unnecessary biopsies that often result from false-positive PSA tests. For example, he says, some 15% of initial PSA tests show elevated PSA, which leads to a first biopsy for those men. Yet, only 25% to 30% of that group actually has clinical signs of cancer.

Gen-Probe’s new test holds the promise of being a more accurate predictor of the biopsy result. “The test is not yet approved by the FDA,” Dr. Rittenhouse cautions, but it appears to have 75% to 80% specificity, versus 25% to 30% for PSA. PCA3 tests are being sold by two reference labs as analyte-specific reagents. Studies are going well in Europe, he says, and Europe’s CE mark is anticipated before year’s end. In the U.S., the company has met with the FDA to discuss the research and to design the appropriate studies.

Further out, Gen-Probe is in the early stages of developing molecular assays targeting the common, recurrent gene translocations it has found in prostate cancer discovered recently at the University of Michigan and confirmed by other researchers. Dr. Rittenhouse says that early work indicates that “they are very specific to cancer and have not been found in premalignant tissue.”

bioMerieux recently launched a 1,000-woman trial to identify early-stage breast cancer from whole blood. The goal is to develop a more convenient and more sensitive screening method that can be implemented more easily than mammography. As Dr. Kaspar points out, “compliance in mammography is still too low, and sensitivity differs among age groups, as younger women have denser breast tissue than older women.” Earlier results obtained with its partner, ExonHit Therapeutics (, showed an overall accuracy of 87%.

Other bioMerieux projects include developing “a whole range of products dedicated to respiratory disease, including the recently launched H5N1 RUO reagent, assays for other high-value infectious disease segments that are transversally connected with products in our other technology segments, integrated systems solutions that ease the workflow in the laboratory, and products with applications in oncology for screening, stratification, and follow-up.”

Real-time Diagnostics

Prodesse (, with its line of analyte-specific reagents in the U.S. and CE-marked kits in Europe, is tightly focused on real-time diagnostics. Last March, the company launched the Pro hMPV™ CE-marked kit in Europe and analyte-specific reagents in the U.S. to detect human metapneumovirus (hMPV).

That makes it “one of only a handful of manufacturing labs globally licensed for an hMPV detection product,” says Tom Shannon, CEO. “We have the only commercially available real-time molecular-based licensed PCR analyte-specific reagents for labs to use to design, develop, and validate their own assays to detect hMPV.”

Other Prodesse products can use four channels in a real-time thermocycler with multiple dyes to detect three organisms plus the control. “We have single reaction tests for influenza A, B, RSV, M. pneumoniae, and C. pneumoniae.” Traditionally, it takes weeks to culture mycoplasma pneumoniae. “Our products help the lab tests that achieve results within three to five hours.”

Newer products may include Invitrogen’s( LUX platform in addition to Roche’s ( 5´ Taqman® platforms to expand their potential use on additional real-time thermocyclers. “Our reagents currently are compatible with five different machines and some have been modified for microarrays,” Shannon says.


Last April, AdvanDx ( launched Evigene™ kits to detect specific antibiotic resistance, virulence, and toxicity markers in such bacteria as methicillin-resistance (MRSA), Panton Valentine leukocidin (community-acquired MRSA), and TSST-1 (toxic shock syndrome toxin 1). “These qualitative hybridization assays are based upon nucleic acid signal amplification for three-hour detection of gene markers in S. aureus and enterococci isolates. The kits are available for research use in the U.S. and may be available for clinical use by mid-2007,” according to Philip Onigman, director of sales and marketing.

Next year, Onigman suggests AdvanDx’ PNA FISH platform will include tests for Gram negative bacteria, including E.coli and Pseudomonas. Used to rapidly identify specific bacteria species directly from positive blood cultures, the PNA FISH assay uses fluorescence-labeled probes targeting the bacteria’s rRNA. Results are available within a few hours.

Cytocore ( currently is assessing the feasibility of using P2X7 to differentiate between normal and cancerous uterine cells, according to George Gorodeski, M.D., Ph.D., scientific adviser for Cytocore and professor of reproductivie biology, oncology, physiology, and biophysics, Case Western University. “P2X7 is expressed in higher levels in normal cells than in cancerous cells,” he says. Its inhibitor, a naturally expressed, truncated version called P2X7-j, however, expresses at steady levels, leading to speculation that it is a mechanism that blocks production of P2X7. Potential applications are being investigated.

The growth in molecular diagnostics means that “what used to be hard and esoteric is being done now in hospitals labs,” according to Mary Beth Carpenter of Focus Diagnostics ( “Any new product ought to be very disease-specific and should help in diagnosis, not just detecting a pathogen but determining what the presence of that pathogen means in context.”

GenomEX™, launched last November, does just that for cystic fibrosis. It is designed for hospitals and commercial labs capable of genetic testing but lacking a board-certified molecular geneticist. Additional diseases will be added gradually.

In addition to Abbott Molecular’s ( established, complementary assay to determine the appropriateness of beginning a Herceptin regimen (based on the presence of the her2 gene) to treat metastatic breast cancer, the company is developing molecular tests for EGFR amplification and for bladder cancer. The latter uses FISH technology to determine early recurrence of bladder cancer. “It should be on the market in a couple of years,” Don Braakman of Abbott Molecular predicts.


Automation is also becoming important in molecular diagnostics. At Abbott that means automated sample prep and data analysis through the M-200 automated Real Time PCR system. The first applications are for HIV, hepatitis C, Chlamydia, and gonorrhea. The system is available in Europe and is expected to be introduced in the U.S. later this year for HIV and hepatitis C, according to Braakman.

“Automated real-time PCR removes the barriers, making testing easier and more efficient for diagnostics labs,” Braakman says. “Automating sample prep, DNA amplification, and data analysis resulted in an overall time reduction of 75 percent from start to finish.”

“We’re at the point,” Dr. Wassman says, “where the tools are letting molecular diagnostics evolve into a practical service in a lab,” but many kits don’t contain the expertise to help physicians or lab analysts interpret the results. Thus, physician inertia is the biggest challenge, Onigman says. To overcome that, physicians need to better understand the practical application of molecular assays.

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