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Oct 15, 2005 (Vol. 25, No. 18)

Molecular Diagnostics as Clinical Tools

New Applications Help Research Advance to Full Bedside Utility

  • Molecular diagnostics is becoming a driving force in drug development. Applications have spread from identifying infections to include screening for cancer, hepatitis, and a variety of genetic disorders, and even tissue screening to minimize the risks of tissue rejection, according to speakers at the IBC Conference, "Molecular Diagnostics and Personalized Medicine" in Boston last month.

    "The scientific community is progressing quite rapidly in developing molecular diagnostics, and industry is developing assay prototypes and conducting larger validation studies to advance this research to full clinical utility," according to Marcia Lewis, Ph.D., senior director of oncology programs, Celera Diagnostics (www.celeradiagnostics.com).

    "Pharmaceutical companies are feeling their way through this, often with third party biotech partners," according to Angus Hastie, director, marketing and business development, Roche Molecular Diagnostics (www.roche-diagnostics.com).

    Roche has a dedicated initiative, SynergysDx, to develop collaborative Rx/Dx programs. Only a few of the larger companies are taking a top-down approach to directly incorporate pharmacogenomics into their development pipeline.

    In developing molecular diagnostics the criticaland most often overlookedsteps, Dr. Lewis says, are methods standardization and the collection of routine sample types.

    "Standardization is needed so meta-analyses can be performed more accurately. Recent breast cancer prognostic studies, for example, have different clinical endpoints, technology platforms, and approaches to statistical analysis, and have included different genes.

    "Most of those gene combinations or signatures don't overlap, and the studies failed to use readily available samples. The results, therefore, are difficult to compare. Some efforts towards standardization to resolve these disparities are underway, but the field is crying for standardization," she says.

    A recent study, conducted by researchers from the Royal North Shore Hospital in Australia and the University of Calgary in Canada, concluded that 69% of meta-analyses in critical care have serious flaws. Results were similar for emergency medicine, anesthesia, and general surgery.

  • Broad Opportunities

    As the field of molecular diagnostics emerges, Dr. Lewis says she sees two broad opportunitiesone in genotyping for patients for stratification and the other in expression profiling for patient monitoring.

    Patient stratification encompasses predisposition to disease, disease type, progression, drug selection, dose selection, and toxicity avoidance. Patient monitoring could include disease initiation, progression, severity, drug efficacy, and drug toxicity.

    Celera Diagnostics is developing a "useful and highly predictive" gene panel for breast cancer prognosis. The panel relies on carefully selected reference genes that don't vary in cancer, so results are expected to be more reproducible than those derived from similar tests. Panel genes also are balanced to interrogate several different biological pathways.

    Currently, Celera Diagnostics is working with pharmaceutical companies to develop tests to measure drug resistance, to help determine patient eligibility for certain drugs, and to develop predictive drug response tests.

    "Rigorous statistical analysis, combined with traditional prognostic factors such as age, size of tumor, and hormone receptor status will be key to determining the independent contribution of a gene expression profile," explains Dr. Lewis, and "the fewer diagnostic markers you have in a test, the simpler it is to run and analyze the data."

    Celera is now determining the medical utility of the test, through large scale validation studies.

    Molecular diagnostics has the potential to help companies make faster decisions for drugs in clinical development and to identify patients, who will or will not respond to given treatments, according to Parul Doshi, Ph.D., associate director, molecular profiling group, Pfizer (www.pfizer.com).

    The need, she maintains, is to identify what determines whether a patient will respond to a given treatment. "Molecular diagnostics actually exist for oncology," Dr. Doshi emphasizes, and are quite effective.

  • Quicker Decision Making

    The International Randomized Interferon study of chronic-phase chronic myeloid leukemia, for example, showed that 98% of patients receiving Novartis' (www.novartis.com) Gleevac (in combination with Interferon and cytarabine) had a complete hematologic response at 48 months. More traditional therapies consider a 1015% efficacy rate to be very good, she adds.

    The goal is to translate such successes to other diseases and other therapies.

    "Whether we can characterize the molecular phenotype of a tumor and identify the underlying causes of disease and then develop effective therapies," is the issue, according to Dr. Doshi. The flip side, of course, is that specific molecular therapies are effective in only the small percentage of the patient population that has those specific molecular characteristics.

    Pfizer currently is looking for the molecular phenotype of tumors related to its pipeline to develop more effective therapies, and also to enhance the developmental process and clinical therapies in its portfolio.

  • Impact on Market

    There is a sentiment in the pharmaceutical industry that molecular diagnostics and pharmacogenomics will reduce the patient populationand the marketfor many medications, but that's not accurate, according to Hastie, at Roche Molecular Diagnostics.

    He says that, so far, although the science is becoming rapidly understood and the regulatory momentum is growing, the industry is lacking clarity regarding the specific fiscal value that a diagnostic will bring to a drug. "It's true," he says, that "you eliminate trial and error revenue with a diagnostic, but you can affect return on investment in a positive way."

    Using case-based reasoning methodology, developed by Ireland-based Diaceutics (www. diaceutics.com), the model Hastie is developing indicates that companies can realize several drivers that may improve a drug's success in the marketplace by increasing diagnostic accuracy, speeding the adoption rate, and simultaneously improving compliance. These advantages can be achieved, he says, "by targeting a more enriched patient population via a diagnostic that screens pre-treatment for response prediction," and by developing monitoring diagnostics that are linked to specific drugs.

    "Patients have a better response, so they are more likely to take it," he says. Also, associating a diagnostic with a drug "allows market expansion by targeting more diseased patients, identifying patients who were misdiagnosed, and identifying subsets of patients by probability of response or the likelihood of havingor not having adverse side effects," which often become known years after the trials and sometimes result in significant corporate liability, as in the Vioxx situation.

    "Case-based reasoning takes the guesswork out of the fiscal assessment," Hastie says, by finding real-world cases, pooling them, and examining the trends. Roche is developing a hypothetical case study, based on rheumatoid arthritis and the DMARD class of drugs.

    Applying molecular diagnostics to therapeutics is feasible for both launched and not-yet-launched drugs but, ideally, occurs before a drug is launched.

    "There is more leverage at that point in terms of pricing decisions and identifying optimal indications for approval," according to Hastie.

    Applied to launched drugs, diagnostics can contribute to additional indications and subsequent label amendments. It may then be possible for a drug to seek marketing exclusivity or patent extension, based on these new indications.

  • Assisting Drug Development

    AstraZeneca (www.astrazeneca.com) is capitalizing on another aspect of molecular diagnostics that's rarely mentioned. It has the potential to develop drugs that are suitable for most patients and, simultaneously, to increase the efficiency of the drug development process. Ruth March, Ph.D., senior principal scientist, R&D genetics, notes that AstraZeneca applies genetics "right from the beginning," to ensure the company is working with the most common forms of target proteins.

    Often, Dr. March says, "the sequences in the databases aren't the most common," in the patient population. Instead, "We genetically screen a pool of DNA from the likely patient populations when developing drugs," she elaborates. Using these common proteins helps identify the most promising drug candidates, and thus "minimizes unexpected clinical variations that are due to population diversity," Dr. March says.

    "The use of molecular diagnostics may not always be necessary," continues Dr. March, if the focus of drug development is on drugs that work for broad populations.

    Drug candidates that interact with common cytochrome P450 genes are a prime example. These genes are responsible for the metabolism of about 50% of older drugs, but they vary among populations. By screening for these interactions in automated systems, drug candidates can be selected that either don't depend on these polymorphic enzymes or that can be flagged as having potential clinical issues, notes Dr. March.

    "AstraZeneca scientists have been involved in both types of research, demonstrating that the safety and efficacy of omerazole was not affected by genetic variations, and also exploring the relationship between tumor mutation status and response to cancer drugs," she points out. Conducting such research, however, requires genetic samples.

    The issues involved in obtaining those samples is spawning an influx of new regulations throughout Europe that is slowing the pace of genetic research there, notes Dr. March, because members of institutional review boards are putting part of their work on hold while they wait for clarification and regulatory harmonization.

    Hepatitis C patients are beginning to reap the benefits of molecular diagnostics now, thanks to consensus management statements issued in France, the U.S., and Taiwan, and other countries. Although the molecular assays have been available for several years, it took issuance of these guidelines for the tests to take hold among physicians, according to David Hendricks, Ph.D., director and senior research fellow, Bayer Diagnostics (www.bayerdiag.com).

    The key to that acceptance was the "2 log10" stopping rule, he says. Each of the statements, issued separately, strongly advises that treatment be halted if, at week 12 of therapy, the hepatitis C viral load has not been reduced by at least two logs, to concentrations roughly one percent of baseline. Because therapy was given a clearly-defined stopping point based on viral load, physicians had a reason to use quantitative molecular tests.

  • Refining Diagnosis

    Typically, Dr. Hendricks explains, when a patient presents with the possibility of hepatitis C, the physician conducts a battery of tests, including an antibody test that shows exposure to hepatitis C virus. Consensus guidelines also call for an HCV RNA test to indicate viral persistence, and thus, to confirm the diagnosis.

    Refining that diagnosis to identify the specific genotype is extremely important.

    "This is where molecular diagnostics also kicks in," explains Dr. Hendricks. Hepatitis C has six major genotypes, which can be divided further into subtypes. Genotype 1 and, sometimes, genotype 4, are treated differently from all the other genotypes.

    "With Genotype 1, therapy lasts 48 weeks. For non-one genotypes, therapy lasts 24 weeks, as a rule of thumb," he says. Baseline testing, therefore, has two components genotyping and quantification of HCV genotype 1 virus.

    Therapies have advanced dramatically in the past decade, as cure rates have climbed from 15%, with interferon for 12 months of treatment in 1992, to 55%, with a combination of pegylated interferon and ribavirin in 2002, reports Dr. Hendricks.

    Consequently, "pegylated interferon and ribavirin are used most often in therapy," despite some nasty side effects.

    Those side effects and the cost of treatment spurred the consensus committees to call for another quantification test at week 12. If there is less than a 2 log10 change in the viral load, stopping treatment is strongly recommended.

    "Almost no one is cured past that point, even with the full course of therapy, without that drop in viral load," Dr. Hendricks explains. "To detect a 2 log10 change in viral load, quantitative HCV RNA assays must be linear and reproducible," and, ideally, have a wide dynamic range.

    "At the end of the therapy, you run a more sensitive assay, a qualitative HCV RNA assay, which says a virus is or is not detected. Six months after completion of therapy, patients are tested again," to determine whether the clearance of virus is sustained.

    If the virus is not detected, the patient is considered to be cured. Ultra-sensitive qualitative HCV RNA assays may provide additional value by detecting the virus during, or at the end of therapy, when HCV is missed by less sensitive assays. Trials are needed, he says, to determine whether such assays would provide real clinical benefit.

    According to K.K. Jain, M.D., founder, Jain PharmaBiotech (Basel, Switzerland), some 500 companies are involved in molecular diagnostics, and account for a $6.5 billion global market this year. By 2010, that figure is expected to increase to $12 billion.

    By $2015, he predicts a global market of $35 billion for molecular diagnostics.



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