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Molecular Diagnostics (molecular + diagnostics)
Selected AbstractsMolecular diagnostics of non-small cell lung cancer using mediastinal lymph nodes sampled by endoscopic ultrasound-guided needle aspirationCYTOPATHOLOGY, Issue 1 2006M. Al-Haddad Non-small cell lung cancer is a common cancer with significant mortality. Accurate and early staging of this cancer has a significant impact on outcome. Endoscopic ultrasound-guided fine needle aspiration of involved mediastinal lymph nodes is critical for staging. Several molecular markers have been identified recently in association with non-small cell carcinoma of the lung that are promising to make early detection of metastatic disease more reliable. [source] Diagnosis, clinical features and molecular assessment of the dysfibrinogenaemiasHAEMOPHILIA, Issue 5 2008M. HILL Summary., Hereditary dysfibrinogenaemia is characterized by the presence of functionally abnormal plasma fibrinogen. Dysfibrinogenaemia is a heterogeneous disorder associated with different mutations throughout the three genes that code for the fibrinogen sub-units, affecting many different aspects of fibrinogen/fibrin activity. Dysfibrinogenaemia may be discovered during the investigation of individuals who present with bleeding or thombosis, or may be found in individuals during routine coagulation screening. More specialized coagulation tests may confirm the diagnosis of dysfibrinogenaemia but do not reliably distinguish between the different fibrinogen variants and are not usually useful in predicting bleeding or thrombotic risk. Advances in molecular diagnostics have facilitated the investigation of the molecular causes of fibrinogen disorders. Several ,hot spot' areas have been identified where mutations causing a high proportion of cases of dysfibrinogenaemia are found (A,Arg16 and ,Arg275). Molecular diagnostics have also shown that many fibrinogen variants share the same causative mutation. There is a discrepancy between the quality of the molecular and functional data available for each mutation and the clinical information on individuals and their family members. However, there are accumulating data that the ,hot spot' mutations accounting for 60,80% of cases of dysfibringenaemia are not associated with a significant bleeding or thrombosis in the absence of other risk factors. Rapid screening for these mutations may provide reassurance for patients in the presurgical setting. [source] Cytologic diagnosis of osseous lesions: A review with emphasis on the diagnosis of primary neoplasms of boneDIAGNOSTIC CYTOPATHOLOGY, Issue 4 2009Lester J. Layfield M.D. Abstract Fine-needle aspiration has been utilized as the initial diagnostic technique at a large number of body sites for over three quarters of a century. As early as the 1930s, fine-needle aspiration (FNA) was used to investigate lesions of the musculoskeletal system. In many early reports, FNA was most frequently and successfully used for the diagnosis of metastatic disease to bone. Less emphasis was placed on its utility for the investigation of primary neoplasms of bone and soft tissue. Current utilization of FNA continues to de-emphasize its application to the diagnosis of primary lesions of the musculoskeletal system. Recent advances in imaging techniques, immunohistochemistry, and molecular diagnostics along with an increasing familiarity among pathologists with the cytologic appearance of primary osseous tumors has led to reevaluation of the technique for investigation of these tumors. The diagnostic accuracy of FNA along with its relatively low cost and high degree of safety makes it a desirable technique for the investigation of primary lesions of the musculoskeletal system. This article reviews issues of diagnostic accuracy, optimal practice procedures, and benefits of the technique including cost reduction. The article will review criteria for selection of appropriate tissue targets for FNA to reduce the number of unsatisfactory specimens. Cytomorphologic features of the more common primary neoplasms of bone will be summarized along with recommendations for the utilization of immunohistochemistry and molecular diagnostics in the work-up of primary neoplasms of bone. Diagn. Cytopathol. 2009. © 2009 Wiley-Liss, Inc. [source] A systems biology approach to understanding atherosclerosisEMBO MOLECULAR MEDICINE, Issue 3 2010Stephen A. Ramsey Abstract Atherosclerosis, a chronic inflammatory disease of the vascular system, presents significant challenges to developing effective molecular diagnostics and novel therapies. A systems biology approach integrating data from large-scale measurements (e.g. transcriptomics, proteomics and genomics) is successfully contributing to deciphering regulatory networks underlying the response of many different cellular systems to perturbations. Such a network analysis strategy using pathway information and data from multiple measurement platforms, tissues and species is a promising approach to elucidate the mechanistic underpinnings of complex diseases. Here, we present our views on the contributions that a systems approach can bring to the study of atherosclerosis, propose ways to tackle the complexity of the disease in a systems manner and review recent systems-level studies of the disease. [source] Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolutionENVIRONMENTAL MICROBIOLOGY, Issue 4 2009Satoshi Ishii Summary A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or ,fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution. [source] Diagnosis and detection of host-specific forms of Fusarium oxysporum,EPPO BULLETIN, Issue 3-4 2000R. P. Baayen Diagnosis and detection of host-specific forms of Fusarium oxysporum are traditionally based on the combination of diagnostic symptoms on the host with the presence of the fungus in the affected tissues. The classical approach is becoming increasingly problematic because more than one forma specialis may occur on a given host, along with non-pathogenic strains which are common soil and rhizosphere inhabitants. Neither formae speciales nor pathogenic races within formae speciales can be distinguished morphologically. Although united by joint pathogenicity to a given host, strains belonging to the same forma specialis need not be phylogenetically related. Development of diagnostics for host-specific groups in F. oxysporum requires monophyletic target groups. Recent studies on gene-genealogy and AFLP-based phylogenies show that the majority of formae speciales in F. oxysporum are polyphyletic (unnatural) and do not offer any prospects for the development of molecular diagnostics. In contrast, highly specific PCR primers have been developed for formae speciales (or races) that consist of a single clonal lineage, and for monophyletic groups of lineages within a forma specialis. Among others, specific PCR primers have thus been developed for F. oxysporum f. sp. basilici, specific races in F. oxysporum ff. spp. dianthi and gladioli, and for the EPPO A2 (EU II/A1) quarantine fungus F. oxysporum f. sp. albedinis which can reliably replace conventional isolation and pathogenicity testing procedures. [source] Molecular genetics of Xeroderma pigmentosum variantEXPERIMENTAL DERMATOLOGY, Issue 5 2003Alexei Gratchev Skin abnormalities result from an inability to repair UV-damaged DNA because of defects in the nucleotide excision repair (NER) machinery. Xeroderma pigmentosum is genetically heterogeneous and is classified into seven complementation groups (XPA-XPG) that correspond to genetic alterations in one of seven genes involved in NER. The variant type of XP (XPV), first described in 1970 by Ernst G. Jung as ,pigmented xerodermoid', is caused by defects in the post replication repair machinery while NER is not impaired. Identification of the XPV gene was only achieved in 1999 by biochemical purification and sequencing of a protein from HeLa cell extracts complementing the PRR defect in XPV cells. The XPV protein, polymerase (pol),, represents a novel member of the Y family of bypass DNA polymerases that facilitate DNA translesion synthesis. The major function of pol, is to allow DNA translesion synthesis of UV-induced TT-dimers in an error-free manner; it also possesses the capability to bypass other DNA lesions in an error-prone manner. Xeroderma pigmentosum V is caused by molecular alterations in the POLH gene, located on chromosome 6p21.1,6p12. Affected individuals are homozygous or compound heterozygous for a spectrum of genetic lesions, including nonsense mutations, deletions or insertions, confirming the autosomal recessive nature of the condition. Identification of POLH as the XPV gene provides an important instrument for improving molecular diagnostics in XPV families. [source] Specific Colorimetric Detection of Proteins Using Bidentate Aptamer-Conjugated Polydiacetylene (PDA) LiposomesADVANCED FUNCTIONAL MATERIALS, Issue 18 2010Yun Kyung Jung Abstract The development of a bidentate aptamer-functionalized polydiacetylene (PDA) liposome sensor that is capable of specific colorimetric detection of proteins, directly in complex mixtures (e.g., serum), at sub-micromolar concentrations within 15 min, is reported. In comparison to sensors fabricated with a single aptamer reagent, the conjugation of bidentate aptamer pairs that recognize two distinct exosites of the target protein (thrombin) to the liposome results in significant enhancements of the sensitivity and the specificity. To elucidate the mechanism behind this enhancement, experimental evidence is presented that suggests that the liposomic aggregation triggered by specific, multi-site binding to the target protein is responsible for the improved colorimetric response. Since the colorimetric protein sensor does not require any power or instrumentation, it offers a promising approach towards molecular diagnostics at point-of-care (POC), especially in low-resource settings. [source] Nanoporous Copper with Tunable Nanoporosity for SERS ApplicationsADVANCED FUNCTIONAL MATERIALS, Issue 8 2009Lu-Yang Chen Abstract Nanostructured materials with designable microstructure and controllable physical and chemical properties are highly desired for practical applications in nanotechnology. In this article, it is reported that nanoporous copper with a tunable nanopore size can be fabricated by controlling the dealloying process. The influence of acid concentration and etching potential on the formation of nanoprosity is systematically investigated. With optimal etching conditions, the nanopore sizes can be tailored from ,15 to ,120,nm by controlling the dealloying time. It is found that the tunable nanoporosity leads to significant improvements in surface-enhanced Raman scattering (SERS) of nanoporous copper and peak values of SERS enhancements for both rhodamine 6G and crystal violet 10B molecules are observed at a pore size of ,30,50,nm. This study underscores the effect of complex three-dimensional nanostructures on physical and chemical properties and is helpful in developing inexpensive SERS substrates for sensitive instrumentations in molecular diagnostics. [source] Diagnosis, clinical features and molecular assessment of the dysfibrinogenaemiasHAEMOPHILIA, Issue 5 2008M. HILL Summary., Hereditary dysfibrinogenaemia is characterized by the presence of functionally abnormal plasma fibrinogen. Dysfibrinogenaemia is a heterogeneous disorder associated with different mutations throughout the three genes that code for the fibrinogen sub-units, affecting many different aspects of fibrinogen/fibrin activity. Dysfibrinogenaemia may be discovered during the investigation of individuals who present with bleeding or thombosis, or may be found in individuals during routine coagulation screening. More specialized coagulation tests may confirm the diagnosis of dysfibrinogenaemia but do not reliably distinguish between the different fibrinogen variants and are not usually useful in predicting bleeding or thrombotic risk. Advances in molecular diagnostics have facilitated the investigation of the molecular causes of fibrinogen disorders. Several ,hot spot' areas have been identified where mutations causing a high proportion of cases of dysfibrinogenaemia are found (A,Arg16 and ,Arg275). Molecular diagnostics have also shown that many fibrinogen variants share the same causative mutation. There is a discrepancy between the quality of the molecular and functional data available for each mutation and the clinical information on individuals and their family members. However, there are accumulating data that the ,hot spot' mutations accounting for 60,80% of cases of dysfibringenaemia are not associated with a significant bleeding or thrombosis in the absence of other risk factors. Rapid screening for these mutations may provide reassurance for patients in the presurgical setting. [source] Novel tools for extraction and validation of disease-related mutations applied to fabry disease,HUMAN MUTATION, Issue 9 2010Remko Kuipers Abstract Genetic disorders are often caused by nonsynonymous nucleotide changes in one or more genes associated with the disease. Specific amino acid changes, however, can lead to large variability of phenotypic expression. For many genetic disorders this results in an increasing amount of publications describing phenotype-associated mutations in disorder-related genes. Keeping up with this stream of publications is essential for molecular diagnostics and translational research purposes but often impossible due to time constraints: there are simply too many articles to read. To help solve this problem, we have created Mutator, an automated method to extract mutations from full-text articles. Extracted mutations are crossreferenced to sequence data and a scoring method is applied to distinguish false-positives. To analyze stored and new mutation data for their (potential) effect we have developed Validator, a Web-based tool specifically designed for DNA diagnostics. Fabry disease, a monogenetic gene disorder of the GLA gene, was used as a test case. A structure-based sequence alignment of the alpha-amylase superfamily was used to validate results. We have compared our data with existing Fabry mutation data sets obtained from the HGMD and Swiss-Prot databases. Compared to these data sets, Mutator extracted 30% additional mutations from the literature. Hum Mutat 31:1026,1032, 2010. © 2010 Wiley-Liss, Inc. [source] Novel COL4A5, COL4A4, and COL4A3 mutations in Alport syndrome,,HUMAN MUTATION, Issue 1 2005Mato Nagel Abstract This study summarizes 47 novel mutations identified during routine molecular diagnostics for Alport syndrome. We detected 34 in COL4A5, the gene responsible for X-linked Alport syndrome, and 13 in COL4A3 and COL4A4, the genes responsible for autosomal recessive Alport syndrome. A high detection rate of 90% was achieved among patients with typical clinical symptoms and a characteristic family history in both X-linked and autosomal recessive forms, and it can be assumed that most relevant mutations have been identified. In numerous positively tested patients, genetic variations which are unknown were detected. © 2005 Wiley-Liss, Inc. [source] Laser-capture microdissection: Applications in routine molecular dermatopathologyJOURNAL OF CUTANEOUS PATHOLOGY, Issue 7 2004Amir S. Yazdi Applications for PCR-based diagnostics are particularly helpful for the determination of clonality in cutaneous lymphocytic infiltrates and for detection of infectious agents, such as herpes simplex virus (HSV), varicella zoster virus (VZV), Borrelia burgdorferi, Mycobacteria, Leishmania, and Treponema pallidum. As biopsies are always composed of different cells, the cells of interest are often only a minor population. As a consequence, their specific DNA is diluted by the majority of contaminating cells. Another problem is the time- and labor-intensive DNA extraction, because usually only formalin-fixed, paraffin-embedded tissue is available, which makes molecular diagnostics a time and labor consuming, and consequently a cost-intensive procedure. To overcome these shortcomings and to eventually shorten the time to generate a result, we introduce a laser-capture microdissection (LCM)-based method for the detection of infectious agents and clonality. Only the cells of interest for the particular indication are microdissected (e.g. epidermal cells for HSV and VZV and lymphocytes for clonality analysis) and subjected to PCR amplification. Due to an accelerated DNA-extraction procedure which generates DNA in 5 h (compared to 3,4 days using conventional DNA extraction), we are able to generate a result within one working day. [source] Current recommendations for the molecular evaluation of newly diagnosed holoprosencephaly patients,,AMERICAN JOURNAL OF MEDICAL GENETICS, Issue 1 2010Daniel E. Pineda-Alvarez§ Abstract Holoprosencephaly (HPE) is the most common structural malformation of the developing forebrain in humans and is typically characterized by different degrees of hemispheric separation that are often accompanied by similarly variable degrees of craniofacial and midline anomalies. HPE is a classic example of a complex genetic trait with "pseudo"-autosomal dominant transmission showing incomplete penetrance and variable expressivity. Clinical suspicion of HPE is typically based upon compatible craniofacial findings, the presence of developmental delay or seizures, or specific endocrinological abnormalities, and is then followed up by confirmation with brain imaging. Once a clinical diagnosis is made, a thorough genetic evaluation is necessary. This usually includes analysis of chromosomes by high-resolution karyotyping, clinical assessment to rule-out well recognized syndromes that are associated with HPE (e.g., Pallister-Hall syndrome, Smith-Lemli-Opitz syndrome and others), and molecular studies of the most common HPE associated genes (e.g., SHH, ZIC2 and SIX3). In this review, we provide current step-by-step recommendations that are medically indicated for the genetic evaluation of patients with newly diagnosed HPE. Moreover, we provide a brief review of several available methods used in molecular diagnostics of HPE and describe the advantages and limitations of both currently available and future tests as they relate to high throughput screening, cost, and the results that they may provide. Published 2010 Wiley-Liss, Inc. [source] Putting the colours into chromogenic in situ hybridization (CISH)THE JOURNAL OF PATHOLOGY, Issue 1 2006J Shipley Abstract Recurrent genomic alterations are the hallmarks of particular cancers. Application of molecular cytogenetic technologies to tumour material in order to detect these alterations has become important for molecular diagnostics and research. A dual-colour chromogenic in situ hybridization (dc-CISH) method described recently in the Journal of Pathology has the advantage of visualizing two probes simultaneously with the ability to discern morphological features. In addition, the bright field microscopy required is readily accessible to many laboratories. The approach has been validated by comparison of results with standard analyses for HER-2 amplification status in formalin-fixed, paraffin-embedded breast cancers and is applicable to the analysis of other clinically relevant genomic aberrations as well as of use in research investigations. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Measles-Associated Encephalopathy in Children with Renal TransplantsAMERICAN JOURNAL OF TRANSPLANTATION, Issue 6 2006A. Turner Two children, boys of 8 and 13 years, presented with measles-associated encephalopathy several years after kidney transplantation for congenital nephrotic syndrome. In the absence of prior clinical measles, the neurological symptoms initially eluded diagnosis, but retrospective analysis of stored samples facilitated the diagnosis of measles-associated encephalopathy without recourse to biopsy of deep cerebral lesions. Each had received a single dose of measles mumps and rubella vaccine before 12 months of age. Prior vaccination, reduction of immunosuppression and treatment with intravenous immunoglobulin and ribavirin may have contributed to their survival. Persistent measles virus RNA shedding, present in one child, was not controlled by treatment with i.v. ribavirin. Two years later, both patients continue to have functioning allografts with only minimal immunosuppression. These cases illustrate the difficulty in diagnosing measles-associated encephalopathy in the immunocompromised host, even in the era of molecular diagnostics, and highlight the renewed threat of neurological disease in communities with incomplete herd immunity. [source] | |||||||||||||||||||||||||