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

Diagnostics in Gene and Protein Expression

Molecular Pathology Segment of the Market Enjoying Steady Growth

  • Molecular diagnostics is a blend of genomics and proteomics tools for studying gene and protein expression. It is well established in infectious disease diagnosis but is becoming increasingly important in the context of inherited genetic disorders, drug development, and personalized medicine. Some of these topics will be discussed in detail at the IBC conference, “Discovery 2 Diagnostics,” in Boston later this month.

    The focus in molecular diagnostics is on developing new applications with already existing technologies. “PCR will continue to be the dominant technology as it adequately addresses low-, medium-, and high-throughput screening of samples in diagnostics testing,” states Stephen Little, Ph.D., CEO of DxS (www.dsxgenotyping.com). DxS offers three PCR-based technologies. The first relies on standard PCR. The second, Scorpions™, is based on real-time PCR, and the third is the Amplification Refractory Mutation System (ARMS™) for detection of gene mutations and SNPs.

    “Our products target detection of acquired mutations. For example, we offer an Epidermal Growth Factor Receptor (EGFR) mutation (an acquired mutation in tumors) kit incorporating Scorpions and ARMS technology. The reaction is based on molecules known as Scorpions that are essentially PCR primers covalently linked to a probe. The probe houses a fluorophore linked to a quencher molecule. During the PCR reaction the fluorophore and quencher separate, resulting in light output from the released fluorophore. The kit allows specific detection of mutations that are present at less than 1% in a heterogeneous sample. It is a sensitive and rapid platform that can generate results in less than three hours,” explains Dr. Little.

    “Molecular diagnostics is a $2-billion market and is rapidly growing. It can be categorized into two areas, infectious diseases and molecular pathology. Infectious disease testing comprises the mature and larger portion of molecular diagnostics market but with slower growth. The smaller portion with faster growth is the molecular pathology segment. It includes the area of oncology, theranostics, personal genomics, and inherited disorders,” says Dwight Denham, business manager of molecular diagnostics at Beckman Coulter(www.beckmancoulter.com). A company representative will be making a presentation at the IBC conference.

    Last year, Beckman Coulter introduced two products for molecular diagnostics applications, the Vidiera™ NsP Nucleic Sample Preparation Platform and the Vidiera NsD Nucleic Sample Detection Platform. The Vidiera NsP is a robotic and validated general-purpose pre-analytical sample-preparation platform that couples nucleic acid isolation, quantitation, normalization, and PCR reaction set-up in a 96-well format, LightCycler® A-rings, and COBAS® Taqman® K-carriers, all in automated mode. It is built on the company’s Biomek® research platform and can handle primary tube blood samples, plasma, serum, and viral transport media (e.g., swabs).

    Automated capillary electrophoresis drives the Vidiera NsD. By separating DNA by size, users can perform fragment-analysis techniques such as STR, SNP analysis, and microsatellite analysis. The post-PCR platform can receive plates directly from thermal cyclers. The platform enables high productivity, as it requires only a five-minute set-up time. It also allows samples to be added in a second plate as the first plate is being processed. The Instrument Controller Software tracks multiple results under the same record, thus it is ideally suited for use in user-defined patient monitoring.

  • Isolation and Preservation for PCR

    Since PCR is lab-oriented, issues such as sample handling, transport, and accessibility to labs are real problems, especially in remote undeveloped areas of the world. Whatman (www.whatman.com) is addressing these issues with its FTA® cards.

    The FTA technology collects, transports, isolates, and preserves nucleic acids at room temperature. It specifically recovers DNA of interest (in this case the pathogenic DNA) by selective lysis of the cells.

    “The FTA is made of cellulosic material pre-treated with chemicals that lyse cells and stabilized onto a matrix that can be integrally preserved at room temperature for several years,” explains Kevin Jones, Ph.D., technical marketing manager of molecular diagnostics at Whatman.

    The other technology is selective lysis of cells to recover only DNA of interest. This technology involves simple filtration optimized by appropriate membrane selection. For example, red blood cells housing the malaria parasite can be separated from white blood cells by simple filtration with glass fiber filters followed by selective lysis.

    Most of the clinical applications of molecular diagnostics are currently in infectious disease testing. Assays for assessing viral loads. However, assays that predict clinical conditions by looking at the human genome or tumors specifically are still in development.

  • Arrays and Bead-based Technologies for Clinical Applications

    CGH arrays, marketed by PerkinElmer (www.perkinelmer.com), function as a result of the comparative genomic hybridization technique. These arrays provide coverage of the entire human genome or specific chromosomal regions. Whole-genome arrays or targeted arrays can be used to look at chromosome structure, copy number, and chromosomal abnormalities that represent disease conditions or inherited disorders.

    “Currently neonatal and prenatal screening is based on protein or metabolite markers. CGH arrays have the potential to serve as a molecular diagnostic tool to fill the gap in genetic screenings in these areas. CGH arrays are a complement to the existing fluorescent in situ hybridization (FISH) technology. CGH arrays are more powerful as they can assess a few hundred markers at one time compared to FISH, which can assess only 5–6 markers at one time. Hence, CGH arrays have applications in cytogenetics and post-natal diagnosis,” explains Howard Grey, Ph.D., director of molecular diagnostics.

    Illumina (www.illumina.com) plans to enter the clinical diagnostics market by the year-end with its VeraCode™ technology. VeraCode utilizes digitally inscribed cylindrical glass microbeads that are 240 µm in length x 28 µm in diameter. The beads are inscribed with holographic elements that diffract light when excited by a laser beam, creating a unique code image. The BeadXpress™ reader, a high-throughput, two-color laser detection system performs bead analysis and detection. The reader scans the beads for their code and fluorescence intensity signals. Data analysis is done with Illumina’s BeadStudio data-analysis software.

    “Since the beads are inscribed, it is a stable technology. This technology can be used in discovery stage to validate markers and track samples or in diagnostic assays to screen for markers. Researchers can custom-tailor their bead arrays in a solution-based format. The multiplexing capability offered by this system makes it suitable for a variety of applications, such as biomarker discovery, SNP genotyping, development of molecular diagnostic assays, gene expression, and protein-based assays,” says Mickie Henshall, product marketing manager for molecular diagnostics at Illumina.

    Invitrogen (www.invitrogen.com) is taking a two-pronged provider and developer approach to enhance its position in the molecular diagnostics arena. The company is an OEM supplier of products that support nucleic acid testing, antibody, flow cytometry, and immunohistochemistry applications of pharmaceutical, in vitro diagnostics firms, and specialty and reference laboratories.

    Some key products marketed by Invitrogen are TAQ polymerases, microarray kits for molecular phenotyping, oligonucleotides, primers, and magnetic beads for the development of nucleic acid and immunoassay formats. The company is now also focusing on developing analyte-specific reagents (ASRs) using a molecular technique known as chromogenic in situ hybridization (CISH).

    “The CISH technology is an alternative to the existing fluorescent in situ hybridization technology, or FISH. CISH, we believe, represents a significant opportunity for us within the anatomic pathology segment of the market,” says Todd R. Nelson, Ph.D., vp of corporate development. “CISH is a flexible molecular technology that allows for the detection of a broad array of gene amplifications and deletions, as well as morphological interpretation using a standard bright field light microscope.

    “Signal stability is longer with CISH technology; the results are 100% concordant with FISH results and can be used effectively in diagnostic tests. We market 30 CISH probes under the SpoT-Light CISH product line and intend to take several of them into the market following regulatory approval. We recently filed our first PMA with the FDA for HER-2 CISH for use as a companion diagnostic for Herceptin therapy.”

    Another interesting product line based on ASR is the LUX™ (Light upon eXtension) reagents for infectious disease screening.

    Invitrogen is also targeting the HLA genotyping market with HLA diagnostics tools, enabled by its recent acquisition of Dynal HLA Diagnostics (www.dynalbiotech.com). These find use in genotyping assays for bone marrow and organ transplantations. Invitrogen sells its RELI, UNITRAY, and SeCore products directly to leading transplant centers worldwide.

  • Personalized Medicine

    “The complexity of clinical tests for application in personalized medicine is a big challenge. Very few molecular tests are FDA cleared or approved. The other challenge is to how link the information obtained from these tests to its clinical utility to achieve the promise of true personalized medicine,” says Melina Cimler, Ph.D., vp of regulatory affairs at Beckman Coulter. Demand for personalized testing is on the rise but there is a learning curve to be crossed by healthcare providers. They need to be educated on the clinical relevancy of these tests so that the resultant information can be used, along with other clinical information for improved individual patient management.

  • Molecular Imaging

    Molecular imaging is a technique that monitors and records the spatiotemporal distribution of molecular and cellular processes for biochemical, biologic, diagnostic, or therapeutic applications. Molecular imaging screens help predict when a patient can develop a disease by comparing baseline levels to elevated levels present in diseased state.

    Since molecular imaging works through analysis of pre-symptomatic marker molecules as opposed to organ (symptomatic) states, it also has direct benefits to patients as one can try improved or experimental drugs that can delay/prevent the onset of disease state.

    GE Healthcare (www.gehealthcare.com) is focusing on molecular imaging to advance molecular medicine. Two key GE Healthcare products in development are F-Angio, an angiogenesis tracer agent, and PIB, for Alzheimer’s disease. These are based on the use of positron emission tomography technology.

    The angiogenesis tracer agent images the neovasculature surrounding a tumor cell. The tracer molecule has an RGD binding region with nanomolar binding affinity to the av/b3 integrin receptor on the cancer-induced angiogenic cell. The peptide is stably bound with radioactive F-18 to allow for positron imaging.

    When injected into a patient it produces image readouts that could be used to detect the extent of disease as well as to monitor the progress of therapy.

    “This molecule is currently in clinical trials and is the first molecular imaging agent of its kind in commercial development,” states Jean-Luc Vanderheyden, Ph.D., global molecular imaging leader at GE Healthcare.

    PIB is a small organic molecule that targets b-amyloid plaque formed during Alzheimer’s disease. “Molecular imaging studies with C-11 labeled PIB in normal, asymptomatic, and Alzheimer’s patients have demonstrated its potential in disease detection and diagnosis. It could help patients that do not exhibit Alzheimer’s symptoms to be diagnosed at early stages, and qualify them as candidates for drugs that can slow down plaque formation,” says Dr. Vanderheyden.



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