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PubMed2005

[Molecular diagnostics in endocrine diseases].

Molecular diagnostic techniques provide an unsurpassed opportunity to understand the pathophysiological basis of endocrine disorders. Diseases have been associated with mutations in almost every gene known to have a role in either the production or secretion of a hormone or the mediators of hormone signalling. Even though most of these mutations are rare and account for only a small fraction of endocrine diseases, molecular diagnostics offers a valuable tool for the clinician in these cases. The most common endocrine disorders such as autoimmune thyroiditis, type 2 diabetes mellitus, osteoporosis, growth disorders, and obesity have all major genetic components, but these are mostly unknown. In this review the clinical implications of molecular diagnostics are illustrated for some endocrine diseases: congenital adrenal hyperplasia, congenital hypothyroidism, thyroid hormone resistance, familial hypocalciuric hypercalcaemia, growth hormone deficiency and resistance, and monogenic obesity. Improved diagnostic specificity has direct implications for treatment and follow up in these syndromes. Molecular diagnostics in endocrine tumours and diabetes are presented in two other articles in this series.

Adrenogenital Syndrome↗
PubMed2003

Molecular diagnostics by microelectronic microchips.

Molecular diagnostics is being revolutionized by the completion of the human genome project and by the development of highly advanced technologies for DNA testing. One of the most important challenges is the introduction of high throughput systems such as DNA chips into diagnostic laboratories. DNA microchips are small devices permitting rapid analysis of genetic information, exploiting miniaturization of all components and automation of operational procedures. The most important biochip applications include gene expression and genetic variation identification and both may improve human molecular diagnostics. Here we review several approaches developed to allow rapid detection of many single nucleotide polymorphisms and mutations in large population samples. Among these, the use of microelectronics seems to best fit with the needs of molecular diagnostics.

Gene Expression Profiling↗
PubMed2004

Molecular diagnostics on lymphoid malignancies.

CONTEXT: Molecular diagnostics for lymphoid malignancies traditionally has focused on helping to provide a diagnosis on a tissue sample. The field has undergone substantial technical and conceptual evolution during the past 2 decades, and its role has expanded to new arenas, such as monitoring disease activities and detecting alterations in genes that are known to have a significant impact on disease outcome. OBJECTIVE: To review the advances in molecular diagnostics on lymphoid malignancies, including recent developments that may facilitate the development of mechanism-based diagnosis for individualized therapy. DESIGN: The development of molecular diagnostics in lymphoid malignancies is briefly reviewed with emphasis on the recent use of gene expression profiling for identifying important diagnostic and prognostic signatures. RESULTS: Genome-scale investigations are becoming technically feasible and have provided promising results in the identification of new disease entities and new, molecularly defined prognosticators. This development can potentially revolutionize diagnostic medicine in the near future. As new genes or genetic pathways that affect the clinical and biologic behavior of tumors are defined and can be readily assayed, molecular diagnostics will be expected to provide this relevant information. Ideally, therapy will be based on this information, delivering the most appropriate treatment with the least toxicity. CONCLUSIONS: Molecular diagnostics in the future will be moving toward a mechanism-based diagnosis for individualized therapy.

Humans↗
PubMed2005

Molecular diagnostics in tuberculosis.

Molecular diagnostics in tuberculosis has enabled rapid detection of Mycobacterium tuberculosis complex in clinical specimens, identification of mycobacterial species, detection of drug resistance, and typing for epidemiological investigation. In the laboratory diagnosis of tuberculosis, the nucleic acid amplification (NAA) test is rapid and specific but not as sensitive as culture of mycobacteria. The primary determinant of successful NAA testing for tuberculosis depends on the shedding of mycobacterial DNA in secretions from caseating granulomas and its dissemination into sterile body fluids or tissue biopsies. In multibacillary diseases with a high mycobacterial load, a positive Ziehl-Neelsen smear with a positive NAA test is diagnostic of active tuberculosis, whereas a positive Ziehl-Neelsen smear with a negative NAA test in the absence of inhibitors would indicate nontuberculous mycobacterial disease. The role of the NAA test is more important in paucibacillary diseases with low mycobacterial loads. The presence of polymerase chain reaction (PCR) inhibitors, however, especially in extrapulmonary specimens, may produce false-negative results. Although this problem can be overcome to some extent by extra extraction steps, the additional processing invariably leads to the loss of mycobacterial DNA. To circumvent this problem, a brief culture augmentation step is carried out before the NAA test is performed, which can enhance the mycobacterial load while concomitantly diluting inhibitors, thereby maintaining the sensitivity of the test without excessively increasing turnaround time.

Microbial Sensitivity Tests↗
PubMed2006

Diagnostic molecular pathology: an increasingly indispensable tool for the practicing pathologist.

CONTEXT: Diagnostic molecular pathology is rapidly becoming an indispensable tool for anatomic pathologists. Familiarity with some of the technologic principles and current, as well as upcoming, molecular diagnostic applications is greatly advantageous for today's practice of pathology. OBJECTIVES: To provide a discussion of the most common techniques currently used in molecular pathology laboratories and review their essential applications to diagnosis and management of neoplastic diseases. DATA SOURCES: A literature review and illustrative cases from the authors' molecular diagnostic practices. CONCLUSIONS: Applications such as clonality assays, molecular cytogenetics, and chimerism analysis are providing us with accurate tools to resolve difficult diagnostic and management decisions in hemato-oncology. This should serve as a future model to expand molecular applications into the wider field of solid tumors.

Chromosome Painting↗
PubMed2005

Molecular diagnostics by microelectronic microchips.

Molecular diagnostics is being revolutionized by the development of highly advanced technologies for DNA and RNA testing. One of the most important challenges is the integration of microelectronics to microchip-based nucleic acid technologies. The specific characteristics of these microsystems make the miniaturization and automation of any step of a molecular diagnostic procedure possible. This review describes the application of microelectronics to all the processes involved in a genetic test, particularly to sample preparation, DNA amplification and sequence variation detection.

Animals↗
PubMed2003

Molecular diagnostics.

It is increasingly evident that molecular diagnostics, that is, the use of diagnostic testing to understand the molecular mechanisms of an individual patient's disease, will be pivotal in the delivery of safe and effective therapy for many diseases in the future. A huge body of new information on the genetic, genomic and proteomic profiles of different hematopoietic diseases is accumulating. This chapter focuses on new technologies and advancements in understanding the molecular basis of hematologic disorders, providing an overview of new information and its significance to patient care. In Section I, Dr. Braziel discusses the impact of new genetic information and research technologies on the actual practice of diagnostic molecular hematopathology. Recent and projected changes in methodologies and analytical strategies used by clinical molecular diagnostics laboratories for the evaluation of hematologic disorders will be discussed, and some of the challenges to clinical implementation of new molecular information and techniques will be highlighted. In Section II, Dr. Shipp provides an update on current scientific knowledge in the genomic profiling of malignant lymphomas, and describes some of the technical aspects of gene expression profiling. Analysis methods and the actual and potential clinical and therapeutic applications of information obtained from genomic profiling of malignant lymphomas are discussed. In Section III, Dr. Liotta presents an update on proteomic analysis, a new and very active area of research in hematopoietic malignancies. He describes new technologies for rapid identification of different important proteins and protein networks, and the potential therapeutic and prognostic value of the elucidation of these proteins and protein pathways in the clinical care of patients with malignant lymphomas.

Cytogenetic Analysis↗
PubMed1999

[Expanding scope and impact of services provided by clinical laboratory practice through molecular diagnostics].

Recent progress in molecular biology and biotechnology has facilitated assays for DNA or RNA sequences to diagnose infectious, neoplastic and genetic diseases. Many of the assays have been used clinically, and are now an essential part of patient care under advanced medicine. A clinical laboratory needs to ensure services for clinical needs such as provision of tests with required turnaround time and high quality as well as consulting practice for individual requests. For quality assurance of assays, it is particularly important to monitor clinical validation of the results by correlating them with the patient's status to prove clinically relevant. Staff need to be trained to become familiar with both molecular pathogenesis and technology so that they can provide informative tests with high quality. Along with advances in pharmacogenomics, the findings of the human genome project have raised the prospect of developing tests for individualized medicine based on genetic information such as those predicting individual susceptibility to diseases to facilitate prevention and indicate responsiveness to drugs for choice of treatment. Molecular diagnostic tests will contribute to an efficient process of decision making on patient care and result in cost savings through earlier and more accurate diagnosis. The scope and impact of services provided by clinical laboratory practice through molecular diagnostics will continue to expand in its integration into clinical practice.

Biotechnology↗
PubMed2005

Molecular diagnostics in melanoma.

Molecular pathology is rapidly evolving, featuring continuous technologic improvements that offer novel clinical opportunities for the recognition of disease predisposition, for identifying sub-clinical disease, for more accurate diagnosis, for selecting efficacious and non-toxic therapy, and for monitoring of disease outcome. Currently, the identification and prognosis of primary cutaneous melanoma is based on histologic factors (tumor depth and ulceration) and clinical factors (number of lymph node and/or distant metastases). However, metastasis can occur in patients with thin melanomas, and sentinel lymph node biopsy does not identify all patients at risk for distant metastasis. New markers exist that correlate with melanoma progression, which may aid in melanoma identification, prognostication, and detection of minimal residual disease/early recurrence. Moreover, not many therapeutic options exist for melanoma as no regimen prolongs survival. Emerging data with investigational therapies suggest that certain markers might play a crucial role in identifying patients who will respond to therapy or show utility in the monitoring the response to therapy. Herein, molecular diagnostics that can potentially benefit the individual melanoma patient will be discussed.

Biomarkers, Tumor↗
PubMed2026

Artificial intelligence in molecular diagnostics for pandemic preparedness.

INTRODUCTION: Molecular diagnostics focusing on the detection and analysis of nucleic acids are indispensable tools for early pathogen identification, transmission monitoring, and genomic surveillance during pandemics. Recent technological advances have broadened the diagnostic landscape, incorporating PCR-based methods, isothermal amplification, high-CRISPR-based amplification detection, and sequencing. Despite their diagnostic potential, widespread implementation remains limited by high validation costs, time and logistical constraints, the need for specialized professional knowledge, and a lack of adaptability in resource-limited settings. Artificial intelligence (AI) is increasingly recognized as a promising but challenging approach, offering tools that streamline assay development, automate data interpretation, and optimize real-time diagnostic performance. AREAS COVERED: This review introduces recently published AI tools with potential to enhance the in-silico design validation process of oligonucleotides for molecular assays. These cover tools for initial assay design and optimization to validation and continuous assay updates. The limitations, including concerns regarding data accuracy, the lack of transparency in data processing ('black box' models), and unresolved licensing and regulatory issues, are highlighted for each tool and as expert opinion. EXPERT OPINION: Collectively, these challenges currently confine most AI-based approaches to research settings and prevent their routine implementation in clinical molecular diagnostics. Their widespread adoption depends on addressing remaining technical, regulatory, and practical challenges.

Humans↗
PubMed2000

Quality assessment in diagnostic molecular pathology: experience from a German-Austrian-Swiss multicenter trial.

In order to assess the current technical standard of diagnostic molecular pathology, we have conducted a multicenter trial with 34 participating pathology laboratories in Germany, Austria and Switzerland. Formalin-fixed, paraffin-embedded tissue blocks were selected from 15 cases, comprising 4 B-cell non-Hodgkin's lymphomas, 4 T-cell non-Hodgkin lymphomas, 4 cases with lymphadenitis, 2 cases with confirmed tuberculosis and 1 case of sarcoidosis. All participating laboratories received one 10-microm section from each of the 15 cases to detect clonality using immunoglobulin heavy chain (IgH) gene or T-cell receptor (TCR)-gamma gene rearrangement analysis in 12 and mycobacterial DNA in 3 cases. In addition, participants had to answer technical questions about the application of internal quality controls and performance of fragment length or sequence analysis. Correct results were reported in 80% and 90% for IgH and TCR-gammagene rearrangement analysis, respectively, and in 83% for mycobacterial DNA analysis. No significant differences in the quality of results were obvious when the individual techniques used for molecular analysis were compared. However, when two independent techniques were used by the same laboratory, a higher rate of correct results was obtained for IgH and TCR rearrangement analysis. In conclusion, this study demonstrates a high technical standard of molecular diagnostic adjuncts among the participating laboratories. Regular multicenter trials with a greater number of participating laboratories working in this field will be indispensable to ensure a continuing or increasing standard in diagnostic molecular pathology.

Austria↗
PubMed2002

Current trends in molecular diagnostics.

Rapid progress in molecular diagnostics is expected to fundamentally change health care. This review of some of the latest innovations covers developments in polymerase chain reaction (PCR), several nonPCR methods, and biochips and nanotechnology, which have accelerated advances in the analysis of nucleic acids and proteins. The greatest impact is likely to be in the integration of diagnosis and therapy and the development of individualized treatment.

Biotechnology↗
PubMed1993

Molecular diagnostics: past, present, and future.

Molecular diagnostics (MDx) is currently a clinical reality that has its roots deep in the study of gene function, structure, and regulation. The multitude of human mutations identified in the various genetic diseases can now be assayed in the clinical molecular diagnostics laboratory. The polymerase chain reaction (PCR) has facilitated the transition from the research to the clinical laboratory, however, many methods which scan and identify known mutations may not be applicable in a clinical environment. A few of these methods are discussed and one technology that is well suited for clinical use is suggested. Well-trained personnel, regulation of MDx laboratories, and automation are a few of the requirements that will carry us into the promising future of molecular diagnosis.

Diagnosis↗
PubMed2000

[Molecular diagnostic tests and chromosome analyses].

Molecular diagnostic tests and chromosomal analyses are often used to diagnose infectious, neoplastic and genetic diseases. However, there are only a few genetic laboratories in university hospitals in Japan because of the high cost and additional staff required for their management. In 1992, we started a genetic laboratory with one technologist in Shinshu University Hospital, and mainly performed polymerase chain reactions(PCR) for the diagnosis of several mycobacterial species, Hepatitis C virus and cytomegalovirus. Infectious diseases diagnosed by PCR have gradually increased over recent years. Chromosome analyses were available in 1996 and spectral karyotyping started from April 1999. Our genetic laboratory was staffed by 4 technologists and 3 faculty members in 1999, and they can provide informative tests with high quality. Molecular diagnostic tests were performed for 855 infectious diseases, 25 hematopoietic tumors and 8 solid tumors, while chromosome analyses were performed for 51 hereditary diseases and 29 hematopoietic tumors in 1998. Establishment of a genetic laboratory in a university hospital may not result in cost savings, but it produces a favorable influence on other laboratories. All staff can use molecular biology techniques to clarify limitations of routine tests and research.

Chromosomes↗
PubMed2006

Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics.

Mutation screening is widely used for molecular diagnostics of inherited disorders. Furthermore, it is anticipated that the present and future identification of genetic risk factors for complex disorders will increase the need for high-throughput mutation screening technologies. Capillary array electrophoresis (CAE) SSCP analysis is a low-cost, automated method with a high throughput and high reproducibility. Thus, the method fulfills many of the demands to be met for application in routine molecular diagnostics. However, the need for performing the electrophoresis at three temperatures between 18 degrees C and 35 degrees C for achievement of high sensitivity is a disadvantage of the method. Using a panel of 185 mutant samples, we have analyzed the effect of sample purification, sample medium and separation matrix on the sensitivity of CAE-SSCP analysis to optimize the method for molecular diagnostic use. We observed different effects from sample purification and sample medium at different electrophoresis temperatures, probably reflecting the complex interplay between sequence composition, electrophoresis conditions and sensitivity in SSCP analysis. The effect on assay sensitivity from three different polymers was tested using a single electrophoresis temperature of 27 degrees C. The data suggest that a sensitivity of 98-99% can be obtained using a 10% long chain poly-N,N-dimethylacrylamide polymer.

Acrylamides↗
PubMed2002

Genetics and molecular diagnostics in the clinical laboratory science curriculum.

OBJECTIVE: To determine the nature and extent of education in human genetics and molecular diagnostics in clinical laboratory science (CLS) programs throughout the U.S. DESIGN: A written survey was mailed to 263 CLS programs. Data were expressed as raw numbers and percentages of responses. SETTING: State University of New York, Upstate Medical University. PARTICIPANTS: There were 162 responses and 151 usable surveys. Most respondents (86.8%) were department chairs/CLS program directors; 13.2% were CLS faculty or educational coordinators. MAIN OUTCOME MEASURES: Questions were designed to determine frequency of CLS programs providing education in genetics, specific molecular methods and clinical applications, format of instruction, satisfaction levels with education provided, and perceptions on importance of teaching genetics, molecular diagnostics, and related hands-on experiences. RESULTS: Over 92% of CLS programs teach human genetics and molecular diagnostics in varied formats. Polymerase chain reaction was the most frequently taught molecular method; microorganism detection, the most commonly taught clinical application. More programs teach theory than provide hands-on experience in molecular diagnostics. Only 59 (39.1%) teach related ethical issues. Sixty-seven respondents (44.4%) were dissatisfied with the education they provide, due to lack of time to teach the material (n = 49; 73.1%), lack of knowledgeable faculty (n = 43; 64.2%), and expense of methods (n = 37; 55.2%). Most respondents felt it was important to include human genetics (n = 145; 96%) and molecular diagnostics (n = 149; 98.7%) in their curriculum, and related hands-on experiences in the student laboratory (n = 106; 70.2%) or clinical rotation (n = 135; 89.4%). Over 82% (n = 124) expected instruction of molecular diagnostics to increase in the next five years. CONCLUSION: Most CLS programs include human genetics and molecular diagnostics in their curriculum, and expect the education they provide to increase in the next 5 years. In order to meet this expectation, CLS programs may need to provide opportunities for faculty training, seek funding to cover the cost of methods, and consider innovative curriculum changes.

Curriculum↗
PubMed2005

Detection of an MEN1 gene mutation depends on clinical features and supports current referral criteria for diagnostic molecular genetic testing.

OBJECTIVE: Diagnostic molecular genetic testing for multiple endocrine neoplasia type 1 (MEN1) has been available since the identification of the MEN1 gene in 1997. Mutation screening of the MEN1 gene has been recommended for patients who meet clinical criteria for MEN1 (at least two of the following: parathyroid hyperplasia, pancreatic endocrine tumour or pituitary adenoma) and those in whom a diagnosis of MEN1 is suspected. We examined the appropriateness of these clinical criteria. PATIENTS AND METHODS: A total of 292 patients were referred for diagnostic testing. The coding region of the MEN1 gene was sequenced in 186 index cases and mutation testing was requested for 106 subjects, including 83 asymptomatic relatives. RESULTS: MEN1 gene mutations were identified in 68/186 index cases (37%). Twenty-nine of the 60 MEN1 mutations reported are novel. The likelihood of finding a mutation was correlated with the number of MEN1-related tumours (mutation detection rate of 79%, 37% and 15% in patients with three, two and one main MEN1-related tumours; P < or = 0.00001) and increased in the presence of a family history (mutation detection rate of 91%, 69% and 29%vs. 69%, 23% and 0% in sporadic cases with three, two or one main MEN1-related tumours, respectively; P < or = 0.00001). The pick-up rate in the 83% of subjects who met proposed criteria for diagnostic testing was 42%, but in those who did not meet these criteria this fell to 0%. CONCLUSIONS: The likelihood of finding an MEN1 mutation depends on the clinical features of the patient and their family. This large series supports present referral criteria for diagnostic mutation screening, but suggests that patients with sporadic isolated tumours rarely have MEN1 mutations.

Adolescent↗