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Molecular diagnostic methods

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https://www.readbyqxmd.com/read/27910874/comprehensive-evaluation-of-molecular-enhancers-of-the-isothermal-exponential-amplification-reaction
#1
Ellie Mok, Eugene Wee, Yuling Wang, Matt Trau
The exponential amplification reaction (EXPAR) is an emerging isothermal nucleic acid amplification method with high potential for molecular diagnostics due to its isothermal nature and high amplification efficiency. However, the use of EXPAR is limited by the high levels of non-specific amplification. Hence, methods that can improve the specificity of EXPAR are desired to facilitate its widespread adoption in practice. Herein, we proposed a strategy to improve EXPAR performance by using molecular enhancers...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910018/fluorescence-in-situ-hybridization-probe-validation-for-clinical-use
#2
Jun Gu, Janice L Smith, Patricia K Dowling
In this chapter, we provide a systematic overview of the published guidelines and validation procedures for fluorescence in situ hybridization (FISH) probes for clinical diagnostic use. FISH probes-which are classified as molecular probes or analyte-specific reagents (ASRs)-have been extensively used in vitro for both clinical diagnosis and research. Most commercially available FISH probes in the United States are strictly regulated by the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), the Centers for Medicare & Medicaid Services (CMS) the Clinical Laboratory Improvement Amendments (CLIA), and the College of American Pathologists (CAP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910012/chromosome-preparation-for-chronic-lymphoid-malignancies
#3
Dorota Koczkodaj, Agata A Filip
Conventional cytogenetics is invariably one of the most important methods used in diagnostics of chronic lymphoproliferations. It complements fluorescence in situ hybridization (FISH) and molecular analysis. Presence of particular chromosomal alterations in chronic lymphocytic leukemia enables patients' stratification into appropriate cytogenetic risk groups and influences treatment decisions. In other non-Hodgkin lymphomas cytogenetic analyses are employed also in minimal residual disease assessment.As lymphocytes in chronic lymphoid malignancies are characterized by low proliferation rate in vitro, it is critical to induce their division in the culture properly...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910009/cancer-cytogenetics-an-introduction
#4
Thomas S K Wan
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27906486/the-fractional-occupation-number-weighted-density-as-a-versatile-analysis-tool-for-molecules-with-a-complicated-electronic-structure
#5
Christoph Alexander Bauer, Andreas Hansen, Stefan Grimme
The fractional occupation number weighted density (FOD) analysis is explored as a general theoretical diagnostic for complicated electronic structures. Its main feature is to provide robustly and fast the information where 'hot' (strongly correlated and chemically active) electrons are localized in a molecule. We demonstrate its usage in four different prototypical applications: (i) As a new and fast measure for the biradical character of polycyclic aromatic hydrocarbons, (ii) for the selection of active orbital spaces in multiconfigurational or complete active space self consistent field (MCSCF/CASSCF) treatments, (iii) as a possibility to consistently describe molecular energy landscapes in regions with varying biradical character as exemplified by partial double bond torsions, and (iv) as a powerful visualization method for static electron correlation effects in large biomolecules in connection with an efficient semi-empirical tight-binding molecular orbital scheme...
December 1, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27904738/recent-developments-in-the-management-of-invasive-fungal-infections-in-patients-with-oncohematological-diseases
#6
REVIEW
Markus Ruhnke, Stefan Schwartz
Patients with hematological cancer have a high risk of invasive fungal diseases (IFDs). These infections are mostly life threatening and an early diagnosis and initiation of appropriate antifungal therapy are essential for the clinical outcome. Most commonly, Aspergillus and Candida species are involved. However, other non-Aspergillus molds are increasingly be identified in cases of documented IFDs. Important risk factors are long lasting granulocytopenia with neutrophil counts below 500/μl for more than 10 days or graft-versus-host disease resulting from allogeneic stem-cell transplantation...
December 2016: Therapeutic Advances in Hematology
https://www.readbyqxmd.com/read/27903301/high-prevalence-of-strongyloides-stercoralis-in-school-aged-children-in-a-rural-highland-of-north-western-ethiopia-the-role-of-intensive-diagnostic-work-up
#7
Aranzazu Amor, Esperanza Rodriguez, José M Saugar, Ana Arroyo, Beatriz López-Quintana, Bayeh Abera, Mulat Yimer, Endalew Yizengaw, Derejew Zewdie, Zimman Ayehubizu, Tadesse Hailu, Wondemagegn Mulu, Adriana Echazú, Alejandro J Krolewieki, Pilar Aparicio, Zaida Herrador, Melaku Anegagrie, Agustín Benito
BACKGROUND: Soil-transmitted helminthiases (hookworms, Ascaris lumbricoides and Trichuris trichiura) are extremely prevalent in school-aged children living in poor sanitary conditions. Recent epidemiological data suggest that Strongyloides stercoralis is highly unreported. However, accurate data are essential for conducting interventions aimed at introducing control and elimination programmes. METHODS: We conducted a cross-sectional survey of 396 randomly selected school-aged children in Amhara region in rural area in north-western Ethiopia, to assess the prevalence of S...
December 1, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27902424/clinical-evaluation-of-mucorales-specific-real-time-pcr-assay-in-tissue-and-serum-samples
#8
Jan Springer, Michaela Lackner, Christian Ensinger, Brigitte Risslegger, Charles Oliver Morton, David Nachbaur, Cornelia Lass-Flörl, Hermann Einsele, Werner J Heinz, Juergen Loeffler
Molecular diagnostic assays can accelerate the diagnosis of fungal infections and subsequently improve patient outcomes. In particular, the detection of infections due to Mucorales is still challenging for laboratories and physicians. The aim of this study was to evaluate a probe-based Mucorales-specific real-time PCR assay (Muc18S) using tissue and serum samples from patients suffering from invasive mucormycosis (IMM). This assay can detect a broad range of clinically relevant Mucorales species and can be used to complement existing diagnostic tests or to screen high-risk patients...
October 24, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27902406/mlvf-as-a-method-for-rapid-and-cost-effective-typing-of-animal-associated-staphylococcus-aureus-strains-from-lineages-other-than-st398
#9
Maja Kosecka-Strojek, Weronika M Ilczyszyn, Aneta Buda, Klaudia Polakowska, Krzysztof Murzyn, Tomasz Panz, Anna Bialecka, Andrzej Kasprowicz, Antoni Jakubczak, Jaroslaw Krol, Alina Wieliczko, Benedykt Wladyka, Jacek Miedzobrodzki
In veterinary medicine, Staphylococcus aureus is associated with a range of mild to severe infections. The high density of livestock in intensive farming systems increases the risk of disease spread and hampers its control and measures of prevention, making S. aureus one of the most important animal pathogens. Multiple-locus VNTR fingerprinting (MLVF) has been successfully applied to the characterization of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) ST398 but not to the characterization of a wide range of other animal isolates...
October 25, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27900251/salivary-biomarkers-in-oral-squamous-cell-carcinoma-an-insight
#10
REVIEW
T Radhika, Nadeem Jeddy, S Nithya, R M Muthumeenakshi
Oral cancer refers to the malignancies that occur in the oral cavity, lip and pharynx with 90% of oral cancers being squamous cell carcinomas (OSCC). OSCC has the highest mortality ratio compared to other carcinomas. Although oral cavity is easily accessible, most oral cancers are detected at a later stage leading to lower survival rates. Early detection of OSCC is a key factor in improving the prognosis and survival rate of the patient. Rapid advancement in the field of diagnosis has enabled early diagnosis of many potentially malignant conditions even before its clinical manifestations...
November 2016: Journal of Oral Biology and Craniofacial Research
https://www.readbyqxmd.com/read/27899992/beside-p53-and-pten-identification-of-molecular-alterations-of-the-ras-mapk-and-pi3k-akt-signaling-pathways-in-high-grade-serous-ovarian-carcinomas-to-determine-potential-novel-therapeutic-targets
#11
Shuhui Chen, Elisa Cavazza, Catherine Barlier, Julia Salleron, Pierre Filhine-Tresarrieu, Céline Gavoilles, Jean-Louis Merlin, Alexandre Harlé
Despite great histological and molecular heterogeneity, the clinical management of high-grade ovarian carcinomas remains unspecialized. As a major subgroup, high-grade serous ovarian carcinomas (HGSOCs) require novel therapies. In addition to utilizing conventional histological prognostic markers and performing oncogenetic investigations, the molecular diagnostic method of next generation sequencing (NGS) was performed to identify 'druggable' targets that could provide access to innovative therapy. The present study was performed in 45 HGSOC patients (mean age, 59...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899111/plasmodium-malariae-in-the-colombian-amazon-region-you-don-t-diagnose-what-you-don-t-suspect
#12
Carlos Hernando Niño, Juan Ricardo Cubides, Paola Andrea Camargo-Ayala, Carlos Arturo Rodríguez-Celis, Teódulo Quiñones, Moisés Tomás Cortés-Castillo, Lizeth Sánchez-Suárez, Ricardo Sánchez, Manuel Elkin Patarroyo, Manuel Alfonso Patarroyo
BACKGROUND: Malaria is a worldwide public health problem; parasites from the genus Plasmodium spp. are the aetiological agent of this disease. The parasite is mainly diagnosed by microscope-based techniques. However, these have limited sensitivity. Many asymptomatic infections are sub-microscopic and can only be detected by molecular methods. This study was aimed at comparing nested PCR results to those obtained by microscope for diagnosing malaria and to present epidemiological data regarding malaria in Colombia's Amazon department...
November 29, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27897025/-nonculture-techniques-of-microorganisms-determination-in-amniotic-fluid-in-patients-with-preterm-prelabor-rupture-of-membranes
#13
R Kutová, L Plíšková, M Kacerovský
OBJECTIVE: The preterm prelabor rupture of membranes is a serious obstetric complication that is frequently complicated by the presence of microorganisms in amniotic fluid. The aim of our work is to characterize current status of nonculture detection of microbial invasion into the amniotic cavity and the experience with the technique performed in University Hospital in Hradec Kralove. DESIGN: Original survey article. SETTING: Institute of Clinical Biochemistry and Diagnostics - molecular biology department, University Hospital Hradec Kralove...
2016: Ceská Gynekologie
https://www.readbyqxmd.com/read/27896485/biomarkers-for-precision-medicine-in-bladder-cancer
#14
REVIEW
Takahiro Kojima, Koji Kawai, Jun Miyazaki, Hiroyuki Nishiyama
Bladder cancer (BC) is classified as non-muscle-invasive BC (NMIBC) or muscle-invasive BC (MIBC). Because the recurrence and mortality rates of BC are high, suitable biomarkers for early detection, evaluation of prognosis, and surveillance of drug responses are needed. Urinary markers simplify surveillance schedules and improve early detection of tumors, especially in NMIBC. Various markers have been identified at DNA, RNA, and protein levels with different sensitivities and specificities. Several biomarkers show a higher sensitivity than urinary cytology, but they are not accurate enough to replace it...
November 29, 2016: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/27895290/comparison-of-phenotypic-and-genotypic-profiles-among-caprine-and-ovine-mycoplasma-ovipneumoniae-strains
#15
Z Maksimović, C De la Fe, J Amores, Á Gómez-Martín, M Rifatbegović
Mycoplasma ovipneumoniae (Movp) is considered to be one of the most important mycoplasmas causing respiratory disease in small ruminants. Most epidemiologic and characterisation studies have been conducted on strains collected from sheep. Information on the presence and characteristics of Movp in healthy and pneumonic goats is limited. Phenotypic or genotypic differences between sheep and goat isolates have never been studied. The objective of our study was to characterise and compare the similarities and differences between caprine and ovine Movp strains isolated from affected and asymptomatic animals in order to elucidate phenotypic and genotypic variability...
November 28, 2016: Veterinary Record
https://www.readbyqxmd.com/read/27894104/proteomic-profiling-of-nci-60-extracellular-vesicles-uncovers-common-protein-cargo-and-cancer-type-specific-biomarkers
#16
Stephanie N Hurwitz, Mark A Rider, Joseph L Bundy, Xia Liu, Rakesh K Singh, David G Meckes
Packed with biological information, extracellular vesicles (EVs) offer exciting promise for biomarker discovery and applications in therapeutics and non-invasive diagnostics. Currently, our understanding of EV contents is confined by the limited cells from which vesicles have been characterized utilizing the same enrichment method. Using sixty cell lines from the National Cancer Institute (NCI-60), here we provide the largest proteomic profile of EVs in a single study, identifying 6,071 proteins with 213 common to all isolates...
November 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27893664/genetic-aspects-of-pituitary-carcinoma-a-systematic-review
#17
Zijiang Yang, Ting Zhang, Heng Gao
BACKGROUND: Pituitary carcinoma (PC) is a rare type of malignant intracranial neoplasm defined as distant metastasis of pituitary adenoma (PA). Although PC incidence is low because only 0.1% to 0.2% of PAs ultimately develop into PCs, the prognosis is poor and 66% of patients die within the first year. Existing therapeutic measures, including surgical removal, chemotherapy, and radiotherapy, have limited effectiveness. The lack of efficacy of current treatments is largely caused by the limited understanding of the molecular pathogenesis of PA and the malignant transformation to PC...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27892737/progress-in-the-molecular-diagnosis-of-lyme-disease
#18
Eva Ružić-Sabljić, Tjaša Cerar
Current laboratory testing of Lyme borreliosis mostly relies on serological methods with known limitations. Diagnostic modalities enabling direct detection of pathogen at the onset of the clinical signs could overcome some of the limitations. Molecular methods detecting borrelial DNA seem to be the ideal solution, although there are some aspects that need to be considered. Areas covered: This review represent summary and discussion of the published data obtained from literature searches from PubMed and The National Library of Medicine (USA) together with our own experience on molecular diagnosis of Lyme disease...
November 28, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27890084/comparison-of-molecular-and-conventional-methods-for-the-diagnosis-of-fasciola-hepatica-infection-in-the-field
#19
Maria Immaculata Arifin, Johan Höglund, Adam Novobilský
The liver fluke, Fasciola hepatica, is one of the major parasite threats to livestock industries world-wide. In sheep and cattle, F. hepatica infection is commonly diagnosed using a range of methods. Aside from conventional coprological and serological diagnostic methods, there are also several molecular methods available based on the detection of liver fluke DNA in faeces. In this study, the outcomes of faecal egg count (FEC), serology and coproantigen ELISA (cELISA) were compared with the performance of polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) in diagnosis of F...
December 15, 2016: Veterinary Parasitology
https://www.readbyqxmd.com/read/27889782/molecular-pathology-a-requirement-for-precision-medicine-in-cancer
#20
Manfred Dietel
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc...
2016: Oncology Research and Treatment
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