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PubMed1998

[Molecular diagnostics by automated systems].

Advent of molecular biology and biotechnology have realized and facilitated analyses for DNA or RNA sequences. New technological advances have led to the automation of major part of the assay process. Automated systems have been developed for amplification and detection of nucleic acid sequence for infectious agents, using polymerase chain reaction, ligase chain reaction, strand displacement amplification, transcription-associated amplification, and nucleic acid sequence-based amplification. Development of such automated systems are based on accumulation and integration of new molecular biotechnology. There has appeared a fully automated PCR system (COBAS AMPLICOR), which amplifies target nucleic acid sequence, captures the biotinylated and amplified products on oligonucleotide-coated paramagnetic microparticles, and detects the products with an avidin-horseradish peroxidase (HRP) conjugate. Automated systems provide improvement of not only labor efficiency but also assay accuracy. Contamination with the amplified products and difficulty in interpreting test results have been overcome with introduction of new technologies such as uracil N-glycosylase and positive internal control. Recently, the extraction of a specific sequence for hepatitis C virus (HCV) RNA has been automated, and the RNA can be specifically extracted from serum by hybridization with probe-coated paramagnetic microparticles, and then subjected to in vitro amplification. Automated systems for nucleic acid extraction from a variety of clinical specimens are now desired. To be practical, an automated system for each molecular diagnostic method must assure assay rapidity, quantification, quality control and cost effectiveness. It is also important to consider how to properly use or combine the molecular diagnostic methods for an efficient approach to the diagnosis of diseases.

Automation↗

PubMed2002

[Molecular diagnostic tools in gastroenterology].

Molecular biology has become an integral part of modern medicine. Novel molecular methods have yielded great progress in early detection, classification and management of a variety of diseases. This review discusses principles and applications of molecular diagnostic tools in the field of gastroenterology.

Adolescent↗

PubMed2002

[Recent advances in molecular diagnostic tests].

Recent advances in molecular biotechnologies have facilitated laboratory use of molecular diagnostic tests. Automated systems for amplification and detection, and lately for extraction, of nucleic acid sequences have been developed. The automated systems have allowed improvement of not only assay efficiency but also quality control of the tests. The information on the genome sequence from the human genome project has been studied to elucidate functions of genes and proteins and the clinical significance of nucleic acid sequences with post-genomics such as expression profiling using DNA microarray, proteomics, and single nucleotide polymorphism analysis, in conjunction with bioinformatics. Now the challenge is the development and application of these new technologies as clinical diagnostic tools. Design of a diagnostic array or panel must be developed with defined sequences based on interpretation of a huge quantity of experimental data to meet clinical demands. There is a need for development of generally available instruments that are inexpensive, practical and more importantly reproducible and reliable.

Computational Biology↗

PubMed1994

Intelligent DNA-based molecular diagnostics using linked genetic markers.

This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system's successful diagnosis of DMD carrier and affected individuals from raw clinical data.

DNA↗

PubMed2005

Clinical impact of molecular diagnostics in low-grade lymphoma.

Molecular diagnostics in low grade B cell lymphoma is currently based on polymerase chain reaction (PCR) detection of lymphoid clonality or of molecular (onco)genetic markers that result from chromosomal translocations. The former is based on detection of clonal immunoglobulin (Ig) and/or T cell receptor (TCR) rearrangements, which can be used for distinguishing between malignant and reactive lymphoproliferation, for staging, for comparison of diagnostic and relapse material and for minimal residual disease assessment. Informativity has risen with the development of improved, standardised DNA-based Ig/TCR strategies but remains dependent on tumour subtype, largely as a function of the rate of IgH somatic mutation. PCR-based detection of molecular genetic markers can aid diagnosis, although genetic breakpoint heterogeneity and low level molecular informativity means that alternative techniques, such as fluorescent in situ hybridisation or immunohistochemistry of the deregulated genes, can be preferable. Appropriate molecular diagnostic practise is entirely dependent on the conservation of appropriate material, with the increasing tendency for RNA based diagnostics, particularly for transcriptional profiling, rendering tissue banking of unfixed material extremely important. Therapeutic stratification of patients with low grade lymphoma is likely to be increasingly based on multiparameter genetic and/or immunological analysis, with monoparameter targets being reserved for follow-up. Appropriate use of the increasing number of analytical techniques available is best applied in specialised diagnostic platforms with a complementary, interdisciplinary approach that can be adapted to the clinical situation.

Clone Cells↗

PubMed1997

Molecular diagnostics.

Nucleic acid technology has assumed an essential role in various areas of in vitro diagnosis. Its major applications include the genomic characterization of mutations and polymorphisms, amplification of nucleic acids by the polymerase chain reaction, analysis of gene expression patterns at the mRNA level, specific detection of mutant proteins, and engineering of proteins used in ligand binding assay. Manipulating the expression of genes in cells and experimental animals allows detailed analysis of processes leading from genomic alterations to disease manifestations and may ultimately yield refinements in diagnostic strategies. The addition of DNA and RNA to the conventional diagnostic in vitro targets and novel approaches to the study of disease processes and manifestations characterize a diagnostic strategy referred to as "molecular diagnostics." This contribution describes some of essential ways in which molecular diagnostics differs from conventional diagnostic approaches. Applications such as differential diagnosis, prenatal diagnosis, early diagnosis, and diagnosis of disease susceptibility are well established in single-gene disorders, and the diagnostic impact of DNA polymorphisms is steadily increasing in multifactorial diseases. The high sensitivity of the polymerase chain reaction makes possible the detection of single infectious agents or tumor cells. With increasing knowledge of expressed gene sequences the expression pattern of mRNA will reflect the biological state of cells with high precision. Mutant proteins can be analyzed based on their structural or biological properties. Use of the appropriate expression systems makes it possible to design proteins for diagnostic in vitro applications such as ligand binding assays.

Aging↗

PubMed2002

[Molecular diagnostic tests availability in view of remuneration for medical services].

By the remarkable development of recent molecular biology and genetic technology, the molecular diagnostic tests had put into practice as the routine test in the field of the clinical laboratory examinations. For molecular diagnostic tests, there are mainly infectious disease, hematological malignancies, hereditary disease, cancers, etc. In especially infectious disease and hematological malignancies, the adaptation of health insurance are examined in the facilities. It is usefully utilized for early detection, early diagnosis, selection of the treatment, follow-up, especially in the hematological malignancies such as leukemia and malignant lymphoma. It is possible to determine the clonal origin of malignant cells, and to detect minimal residual disease (MRD) after achieving complete remission. The usage of the molecular diagnostic tests is variable in infectious disease and hematological malignancies on the medical reimbursement, and there are restrictions like the following; in the case of any tests of the infectious disease, only which or main test can be calculated, facilities standards are necessary in order to calculate the health insurance treatment cost of the once in 6 months. In this article, we describe utilization and restrictions of the medical reimbursement for molecular diagnostic tests, focusing on the fiscal 2002 revision of the medical service fee schedule implemented in April.

Clinical Laboratory Techniques↗

PubMed2002

Molecular diagnostics: hurdles for clinical implementation.

In the coming years, molecular diagnostics will continue to be of critical importance to public health worldwide. It will facilitate the detection and characterization of disease, as well as monitoring of the drug response, and will assist in the identification of genetic modifiers and disease susceptibility. A wide range of molecular-based tests is available to assess DNA variation and changes in gene expression. However, there are major hurdles to overcome before the implementation of these tests in clinical laboratories, such as which test to employ, the choice of technology and equipment, and issues such as cost-effectiveness, accuracy, reproducibility, personnel training, reimbursement by third-party payers and intellectual property. At present, PCR-based testing predominates; however, alternative technologies aimed at reducing genome complexity without PCR are anticipated to gain momentum in the coming years. Furthermore, development of integrated chip devices ("lab-on-a-chip") should allow point-of-care testing and facilitate genetic readouts from single cells and molecules. Together with proteomic-based testing, these advances will improve molecular diagnostic testing and will present additional challenges for implementing such testing in health care settings.

Animals↗

PubMed2003

Nanodiagnostics: application of nanotechnology in molecular diagnostics.

Nanotechnology extends the limits of molecular diagnostics to the nanoscale. Nanotechnology-on-a-chip is one more dimension of microfluidic/lab-on-a-chip technology. Biological tests measuring the presence or activity of selected substances become quicker, more sensitive and more flexible when certain nanoscale particles are put to work as tags or labels. Magnetic nanoparticles, bound to a suitable antibody, are used to label specific molecules, structures or microorganisms. Magnetic immunoassay techniques have been developed in which the magnetic field generated by the magnetically labeled targets is detected directly with a sensitive magnetometer. Gold nanoparticles tagged with short segments of DNA can be used for detection of genetic sequence in a sample. Multicolor optical coding for biological assays has been achieved by embedding different-sized quantum dots into polymeric microbeads. Nanopore technology for analysis of nucleic acids converts strings of nucleotides directly into electronic signatures. DNA nanomachines can function as biomolecular detectors for homogeneous assays. Nanobarcodes, submicrometer metallic barcodes with striping patterns prepared by sequential electrochemical depositon of metal, show differential reflectivity of adjacent stripes enabling identification of the striping patterns by conventional light microscopy. All this has applications in population diagnostics and in point-of-care hand-held devices.

Animals↗

PubMed2004

Molecular diagnostic cytopathology: definitions, scope and clinical utility.

Molecular diagnosis is the application of molecular biology techniques and knowledge of the molecular mechanisms of disease to diagnosis, prognostication and treatment of diseases. Although it is not widely used in routine molecular cytological practice, some examples are presented here of the application of molecular techniques to the routine cytopathological diagnosis of solid tumours and lymphoreticular malignancies. The term 'molecular diagnostic cytopathology' is proposed to define the application of molecular diagnosis to cytopathology, and the challenges of the introduction of molecular diagnosis into routine diagnostic histopathology and cytopathology are discussed. Finally, the importance of a combined morphological, immunophenotypic and molecular approach to maintain the diagnostic pathologist at the heart of the clinical decision-making process is emphasized.

Cytodiagnosis↗

PubMedDate not supplied

Real-time polymerase chain reaction: a novel molecular diagnostic tool for equine infectious diseases.

The focus of rapid diagnosis of infectious disease of horses in the last decade has shifted from the conventional laboratory techniques of antigen detection, microscopy, and culture to molecular diagnosis of infectious agents. Equine practitioners must be able to interpret the use, limitations, and results of molecular diagnostic techniques, as they are increasingly integrated into routine microbiology laboratory protocols. Polymerase chain reaction (PCR) is the best-known and most successfully implemented diagnostic molecular technology to date. It can detect slow-growing, difficult-to-cultivate, or uncultivatable microorganisms and can be used in situations in which clinical microbiology diagnostic procedures are inadequate, time-consuming, difficult, expensive, or hazardous to laboratory staff. Inherent technical limitations of PCR are present, but they are reduced in laboratories that use standardized protocols, conduct rigid validation protocols, and adhere to appropriate quality-control procedures. Improvements in PCR, especially probe-based real-time PCR, have broadened its diagnostic capabilities in clinical infectious diseases to complement and even surpass traditional methods in some situations. Furthermore, real-time PCR is capable of quantitation, allowing discrimination of clinically relevant infections characterized by pathogen replication and high pathogen loads from chronic latent infections. Automation of all components of PCR is now possible, which will decrease the risk of generating false-positive results due to contamination. The novel real-time PCR strategy and clinical applications in equine infectious diseases will be the subject of this review.

Animals↗

PubMed1994

Information engineering for molecular diagnostics.

Clinical laboratories are beginning to apply the recent advances in molecular biology to the testing of patient samples. The emerging field of Molecular Diagnostics will require a new Molecular Diagnostics Laboratory Information System which handles the data types, samples and test methods found in this field. The system must be very flexible in regards to supporting ad-hoc queries. The requirements which are shaping the developments in this field are reviewed and a data model developed. Several queries which demonstrate the data models ability to support the information needs of this area have been developed and run. These results demonstrate the ability of the purposed data model to meet the current and projected needs of this rapidly expanding field.

Clinical Laboratory Information Systems↗

PubMed2006

Microelectronic array system for molecular diagnostic genotyping: Nanogen NanoChip 400 and molecular biology workstation.

Hundreds of gene mutations responsible for Mendelian disorders are currently tested in the clinical laboratory for pre- and postnatal diagnosis, carrier screening and presymptomatic testing. Since human genetic research is currently focused on determining the etiology of complex diseases, including heart disease, diabetes and neuropsychiatric traits, laboratorians will genotype increasing numbers of clinically relevant loci in the future. This will require accurate, high-throughput and cost-effective genotyping platforms, such as the DNA microarray. The Nanogen NanoChip platforms employ hybridization-based technology, using fluorescent detection and electronic control of the target or probe, to obtain clear genotype signal relative to background, and increased flexibility relative to similar chip-based single nucleotide polymorphism genotyping platforms. The scope of this review is intended to describe the operating principle, chips and instrumentation, analyte-specific reagents, published assay protocols, assay development, and clinical use of the NanoChip platforms. It is beyond the scope of this review to describe the use of NanoChip platforms in basic research, and to compare it against all available clinical single nucleotide polymorphism genotyping applications and platforms.

Computational Biology↗

PubMed2004

Molecular diagnostics: a new frontier in cancer prevention.

The promise of molecular diagnostics for cancer prevention in terms of early detection rests on two premises: assays can be developed to measure proteins, DNA, RNA or metabolites that accurately and reproducibly detect incipient neoplasias; and that this early detection will eventually result in a decrease in morbidity and mortality and therefore benefit patients. Novel molecular technologies, including laser capture microdissection, time-of-flight mass spectrometry, DNA microarrays, tissue arrays, protein microarrays and antibody microarrays, are being developed to investigate the molecular differences between disease and normal cells and detect cancer-specific alterations in proteins, DNA and RNA in body fluids. Although literally hundreds of articles are published each year describing alterations in genes or proteins that are associated with cancer, very few result in useful molecular diagnostics for early cancer detection. Thus, there remains a critical need for new biomarkers for use in early detection and for assay methods that allow the translation of these biomarkers from the laboratory to the clinic.

Biomarkers, Tumor↗

PubMed2001

[Molecular diagnostic tests in hematologic diseases].

Molecular diagnostic tests are widely performed in managing hematologic malignancies such as leukemia and lymphoma. In this article, we review the present application and problems of the tests. Karyotyping is performed at diagnosis of all kinds of hematologic malignancies. This method needs dividing cells as samples and skilled experts. Fluorescence in situ hybridization(FISH) analysis using cells in interphase is performed, for example, to monitor the effect of interferon on chronic myelogenous leukemia patients. The weak point of this method is that approximately 2% of false-positive cells are inevitable. Southern blot method is used for clonal analysis in some disease, for example, adult T-cell leukemia/lymphoma. Polymerase chain reaction(PCR) method using genomic DNA is performed for limited types of diseases such as lymphoma with bcl-2/IgH fusion gene. Reverse transcription(RT)-PCR method can detect fusion gene transcripts with high sensitivity. This method is useful for detecting minimal residual diseases after chemotherapy or bone marrow transplantation. To perform quantitative analysis, real-time PCR or competitive PCR must be done. In the near future, new technology such as gene expression profiling analysis using DNA microarrays or spectral karyotyping(SKY) method will be used in clinical practice.

Blotting, Southern↗

PubMed2007

From molecular diagnostics to personalized testing.

Gene-based molecular diagnostics is changing the practice of medicine and will continue to do so for the foreseeable future. The major underlying principle of these diagnostic tests is the use of specific nucleic acid sequences as surrogates; amplification of the surrogate markers enables the detection of pathogens or disease-related gene mutations. Gene targets can be amplified by target-, probe- or signal-based methods. Combined use of nucleic acid amplification and enzyme-linked immunosorbent assay with methods such as immuno-polymerase-chain reaction allows us to detect protein at femtogram (10(15) g) levels. A variety of choices are available for the detection of amplified amplicons with the fluorophore-linked nanoparticles as the most sensitive markers. The unique advantages of using covalently-linked nanoparticles include the detection of single molecules, the ability to enrich molecules of interest with unprecedented detection sensitivity (up to zeptogram levels, 10(21) g) and the flexibility of multiple functionalization. Automation appears to be the current trend for high-volume molecular testing of infectious diseases. Molecular profiling of various diseases using genomic or proteomic approaches opens up a molecule wonderland with promise and emergence of new molecular testing that will likely impact the practice of medicine to a greater degree in the future. The future of molecular-based testing and the journey toward personalized testing will be discussed.

Animals↗

PubMed2001

MEMS-based sample preparation for molecular diagnostics.

Completion of the Human Genome Project is driving the rapid development of molecular diagnostics in the laboratory. To accelerate the penetration of genetic tests and other nucleic acid-based tests into clinical markets, simple, compact, automatic sample-preparation systems for molecular diagnostics must be developed. Microelectromechanical systems (MEMS) is a promising approach for the development of automated sample preparation for the clinical laboratory or point-of-care setting. This review discusses MEMS-based components that could be applied to the different stages of the sample-preparation process such as cell separation, nucleic acid purification, and nucleic acid amplification. Examples of functional component integration are given. Issues discussed include partitioning of functions between the instrument and disposable unit, methods of propulsion of fluids and particles, vapor and liquid barriers, and sample size. Although further evaluation and development are needed to provide practical solutions to some of these issues, we conclude that MEMS-based components might contribute to some components in a sample-preparation system consisting of modular instruments and disposable units, but will not provide a generic or a totally integrated solution.

DNA, Bacterial↗

PubMed2004

Molecular diagnostics in virology.

Molecular biology has significantly improved diagnosis in the field of clinical virology. Virus discovery and rapid implementation of diagnostic tests for newly discovered viruses has strongly beneficiated from the development of molecular techniques. Viral load and antiviral resistance or subtyping assays are now part of the biological monitoring of patients chronically infected by human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV) and CMV. It will be important to add to this panel assays for other viruses of the herpesviridae family. Qualitative assays for the detection of blood-borne viruses have increased safety of blood donation and organ transplantation. Screening of other blood-borne viruses (parvovirus B19, HAV), multiplexing of detection and test automation to improve practicability and reduce costs will be the next steps. A major evolution in the near future will be the generalization of NAT for the diagnosis of viral etiology in patients, mostly with respiratory, CNS or gastro-intestinal diseases. Major technical improvements have been made to avoid obstacles that still limit this generalization, i.e. genetic variability of viruses, multiplex detection, contamination risk. Commercial offers already exist but menus must be extended to limit the validation and documentation work associated with home-brew assays. Real-time amplification has allowed the development of new NAT platforms but automation and integration of all steps of the reaction are still required to reduce hands-on-time, time-to-result and costs, and to increase throughput.

Antibodies, Viral↗