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Molecular diagnostics

Matthew B Lanktree, Bekim Sadikovic, John S Waye, Alexander Levstik, Bruce B Lanktree, Jovana Yudin, Mark A Crowther, Guillaume Pare, Paul C Adams
BACKGROUND: Next-generation sequencing of an iron metabolism gene panel could identify pathogenic mutations, improving on standard hemochromatosis genetic testing and providing a molecular diagnosis in patients with suspected iron overload. METHODS: A next-generation sequencing panel of 15 genes with known roles in iron metabolism was constructed. 190 patients were sequenced: 94 from a tertiary hemochromatosis clinic, and 96 submitted for HFE testing with biochemical evidence of iron overload [elevated ferritin (>450 μg/L) or transferrin saturation (>55%)] obtained from a chart review...
October 18, 2016: European Journal of Haematology
Dagmar Schmitz
Since cell-free DNA (cfDNA) fragments of placental origin can be isolated and analyzed from the blood of pregnant women. Applications of this finding have been developed and implemented in clinical care pathways worldwide at an unprecedented pace and manner. Implementation patterns, however, exhibit considerable insufficiencies. Different "motors" of implementation processes, like the market or various regulatory institutions, can be identified at a national level. Each "motor" entails characteristic ethical challenges which are exemplified impressively by a rising number of case reports...
2016: Advances in Experimental Medicine and Biology
Stefan Holdenrieder
Liquid profiling is a traditional concept in laboratory diagnostics using patterns of blood-derived biochemical molecules for disease detection and characterization. Beyond protein and cellular parameters, molecular biomarkers at the DNA, RNA and miRNA level have been developed as promising diagnostic tools in metabolic and malignant diseases as new technologies for ultrasensitive profiling of nucleic acids in blood and body fluids became available. In cancer disease, they are successfully applied for the stratification of patients for individually tailored therapies, treatment monitoring and the sensitive detection of minimal residual disease...
2016: Advances in Experimental Medicine and Biology
Erina Takai, Yasushi Totoki, Hiromi Nakamura, Mamoru Kato, Tatsuhiro Shibata, Shinichi Yachida
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. The genomic landscape of the PDAC genome features four frequently mutated genes (KRAS, CDKN2A, TP53, and SMAD4) and dozens of candidate driver genes altered at low frequency, including potential clinical targets. Circulating cell-free DNA (cfDNA) is a promising resource to detect molecular characteristics of tumors, supporting the concept of "liquid biopsy".We determined the mutational status of KRAS in plasma cfDNA using multiplex droplet digital PCR in 259 patients with PDAC, retrospectively...
2016: Advances in Experimental Medicine and Biology
Steven Wang, Jie Yan, Guangde Zhou, Rebecca Heintzelman, J Steve Hou
Myeloproliferative neoplasms (MPNs) are hematopoietic malignancies characterized by unchecked proliferation of differentiated myeloid cells. The most common BCR-ABL1-negative MPNs are polycythemia vera, essential thrombocythemia, and primary myelofibrosis. The discovery of JAK2 V617F mutation has improved our understanding of the molecular basis of MPN. The high frequency of JAK2 mutation in MPN makes JAK2 mutation testing an essential diagnostic tool and potential therapeutic target for MPN. Here, we present a rare case of a 34-year-old patient who was initially diagnosed with acute myeloid leukemia (AML) with mutated NPM1...
2016: Case Reports in Hematology
Erika Yeh, Lauren A Weiss
Autism spectrum disorder (ASD) has been long known to have substantial genetic etiology. Much research has attempted to identify specific genes contributing to ASD risk with the goal of tying gene function to a molecular pathological explanation for ASD. A unifying molecular pathology would potentially increase understanding of what is going wrong during development, and could lead to diagnostic biomarkers or targeted preventative or therapeutic directions. We review past and current genetic mapping approaches and discuss major results, leading to the hypothesis that global dysregulation of gene or protein expression may be implicated in ASD rather than disturbance of brain-specific functions...
October 14, 2016: Molecular and Cellular Probes
Maureen O'Sullivan
Since its foundation by remarkably talented and insightful individuals, prominently including Pepper Dehner, pediatric soft tissue tumor pathology has developed at an immense rate. The morphologic classification of tumoral entities has extensively been corroborated, but has also evolved with refinement or realignment of these classifications, through accruing molecular data, with many derivative ancillary diagnostic assays now already well-established. Tumors of unclear histogenesis, classically morphologically undifferentiated, are prominent amongst pediatric sarcomas, however, the classes of undifferentiated round- or spindle-cell-tumors-not-otherwise-specified are being dismantled gradually with the identification of their molecular underpinnings...
September 5, 2016: Seminars in Diagnostic Pathology
Mukundh N Balasubramanian, Nejc Rački, José Gonçalves, Katarina Kovač, Magda T Žnidarič, Valentina Turk, Maja Ravnikar, Ion Gutiérrez-Aguirre
Currently, around 50% of the world's population lives in towns and cities within 100 km of the coast. Monitoring of viruses that are frequently present in contaminated coastal environments, such as rotavirus (RoV) and norovirus (NoV), which are also the major cause of human viral gastroenteritis, is essential to ensure the safe use of these water bodies. Since exposure to as few as 10-100 particles of RoV or NoV may induce gastrointestinal disease, there is a need to develop a rapid and sensitive diagnostic method for their detection in coastal water samples...
October 8, 2016: Water Research
Alireza Najafian, Salem I Noureldine, Faris Azar, Chady Atallah, Gina Trinh, Eric B Schneider, Ralph P Tufano, Martha A Zeiger
BACKGROUND: Molecular markers associated with thyroid malignancy are increasingly being used as differential diagnostic tools for thyroid nodules. However, little has been reported recently regarding the prevalence of these markers in benign lesions. We systematically reviewed the literature to examine studies that reported on the prevalence of these markers in benign thyroid lesions. METHODS: Appropriate papers published between January 01, 2000 and April 30, 2015 and cataloged on PubMed, Embase, Cochrane, Scopus and Web of Science databases by combining different keywords for ''thyroid tumor'' with both general and specific keywords for ''molecular marker'' by using ''AND'' as the Boolean operator...
October 17, 2016: Thyroid: Official Journal of the American Thyroid Association
Michael P Palmer, Rachael Melton-Kreft, Laura Nistico, N Louisa Hiller, Leon H J Kim, Gregory T Altman, Daniel T Altman, Nicholas G Sotereanos, Fen Z Hu, Patrick J De Meo, Garth D Ehrlich
BACKGROUND: Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. AIMS: The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. PATIENTS AND METHODS: Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction-electrospray ionization-time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content...
October 17, 2016: Genetic Testing and Molecular Biomarkers
Juan Xu, Yujia Qian, Min Ye, Ziyi Fu, Xuemei Jia, Wenqu Li, Pengfei Xu, Mingming Lv, Lei Huang, Luyu Wang, Hongjie Ruan, Juan Lv
Endometrial carcinoma (EC) is the most common malignancy in women. Dispite its prevalence, the prognosis of endometrial carcinoma still relies on conventional histological type, grade and invasion information. Its morbidity is still increasing and the outcome is very poor. To the best of our knowledge, hormonal imbalance and/or molecular genetic alterations are the main cause of EC. However, the alterations of lncRNAs which accounts for approximately 4/5 of human transcripts are still poorly understood. In the present study, using the RiboArray™ Custom Array, we studied the expression profiles of lncRNA in EC as compared to normal endometrium (NE) to find potential core lncRNAs for the diagnosis of EC...
October 14, 2016: Oncology Reports
Dae-Weung Kim, Myoung Hyoun Kim, Chang Guhn Kim
In a ProteoChip‑based screening system and subsequent studies, serine‑aspartic acid‑valine (SDV) was demonstrated to specifically bind to integrin αvβ3. An SDV‑containing peptide could target the tumor vessel and it may be an effective replacement for molecular imaging of the tumor. In the present study, a hexapeptide, SDV‑glutamic acid‑cysteine‑glycine (ECG), was developed and evaluated its diagnostic performance as a tumor imaging agent in tumor‑bearing mice. The hexapeptide SDV‑ECG was synthesized using Fmoc solid‑phase peptide synthesis...
October 6, 2016: Molecular Medicine Reports
Anita Chopra, Sushant Soni, Haraprasad Pati, Dev Kumar, Rahul Diwedi, Deepak Verma, Garima Vishwakama, Sameer Bakhshi, Suman Kumar, Ajay Gogia, Rajive Kumar
BACKGROUND & OBJECTIVES: Mutation of nucleophosmin (NPM1) gene in the absence of FLT3-ITD (FMS related tyrosine kinase 3 - internal tandem duplications) mutation carries a good prognosis in cytogenetically normal acute myeloid leukaemia (AML). NPM1, a multifunctional nucleolar phosphoprotein that shuttles between nucleus and cytoplasm, gets trapped in the cytoplasm when mutated. Immunohistochemical (IHC) demonstration of its aberrant cytoplasmic location (NPMc+) has been suggested as a simple substitute for the standard screening molecular method...
June 2016: Indian Journal of Medical Research
Dinesh Singh Tekcham, Satish S Poojary, Shushruta Bhunia, Mustafa Ahmed Barbhuiya, Sanjeev Gupta, Braj Raj Shrivastav, Pramod Kumar Tiwari
BACKGROUND & OBJECTIVES: Loss of function of adenomatous polyposis coli (APC) has been reported in cancer. The two promoters of APC, 1A and 1B also have roles in cancer. But, the epigenetic role of APC promoters is not yet clear in gallbladder cancer (GBC) and gallstone diseases (GSD). We undertook this study to determine the epigenetic role of APC in GBC and GSD. METHODS: Methylation-specific (MS)-PCR was used to analyze the methylation of APC gene. The expression of APC gene was studied by semi-quantitative PCR, real-time PCR and immunohistochemistry (IHC) in GBC, GSD and adjacent normal tissues...
May 2016: Indian Journal of Medical Research
Surbhi Goyal, Kiran Mishra, Urvee Sarkar, Satendra Sharma, Anita Kumari
BACKGROUND & OBJECTIVES: Renal tumours constitute about 7 per cent of all neoplasms in children. It is important to differentiate Wilms' tumour (commonest tumour) from non-Wilms' tumours. The aim of this study was to evaluate the immunoexpression and diagnostic role of Wilms' tumour-1 protein (WT1) in paediatric renal tumours. METHODS: A total of 53 cases of renal tumours in children (below 18 yr) who underwent total nephrectomy were included in this retrospective study...
May 2016: Indian Journal of Medical Research
Ximena Camacho, Victoria Calzada, Marcelo Fernández, Omar Alonso, Roger Chammas, Eloisa Riva, Juan Pablo Gambini, Pablo Cabral
BACKGROUND: Vascular endothelial growth factor (VEGF) is one of the classic factors to tumor-induced angiogenesis in several types, including melanoma. Bevacizumab is a humanized monoclonal antibody directed against VEGF. OBJECTIVE: To radiolabel Bevacizumab with 177-Lutetium as a potential radioimmunotherapy agent for melanoma. METHODS: Bevacizumab was derivatized with DOTA-NHS-ester at 4 ºC for 18 h. DOTA-Bevacizumab was radiolabeled with 177LuCl3 (15 MBq/mg) at 37 ºC for 1 h...
October 10, 2016: Current Radiopharmaceuticals
Clizia Chinello, Vincenzo L'Imperio, Martina Stella, Andrew James Smith, Giorgio Bovo, Angelica Grasso, Marco Grasso, Francesca Raimondo, Marina Pitto, Fabio Pagni, Fulvio Magni
Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids...
October 17, 2016: Expert Review of Proteomics
Emily Hopkins, David Moffat, Ian Parkinson, Peter Robinson, Hubertus Jersmann, Brendan Dougherty, Mohammed I Birader, Kate Francis, Phan Nguyen
BACKGROUND: Rapid on site examination (ROSE) is encouraged at endobronchial ultrasound transbronchial needles aspiration (EBUS-TBNA) to improve diagnostic yield. Due to new therapeutic options in lung cancer, it is not sufficient to merely distinguish between non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC). Immunohistochemistry (IHC) distinction is now standard practice, as well as additional molecular testing where clinically indicated. We investigated the diagnostic yield of on-site smears vs...
September 2016: Journal of Thoracic Disease
Kim E M van Kessel, Willemien Beukers, Irene Lurkin, Angelique Ziel-van der Made, Kirstin A van der Keur, Joost L Boormans, Lars Dyrskjøt, Mirari Márquez, Torben F Ørntoft, Francisco X Real, Ulrika Segersten, Núria Malats, Per-Uno Malmström, Wim Van Criekinge, Ellen C Zwarthoff
PURPOSE: Only 3-28% of patients referred to the urology clinic for hematuria are diagnosed with bladder cancer (BC). Cystoscopies lead to high diagnostic costs and patient burden. Therefore, to improve selection of patients for cystoscopy, reduce costs and over-testing we aimed to validate a recently developed diagnostic urine assay MATERIALS AND METHODS: We included 200 patients from three European countries undergoing cystoscopy for hematuria (n=97 BC, n=103 non-malignant). Voided urine samples were collected prior to cystoscopy...
October 13, 2016: Journal of Urology
Zehra Ordulu, Tammy Kammin, Harrison Brand, Vamsee Pillalamarri, Claire E Redin, Ryan L Collins, Ian Blumenthal, Carrie Hanscom, Shahrin Pereira, India Bradley, Barbara F Crandall, Pamela Gerrol, Mark A Hayden, Naveed Hussain, Bibi Kanengisser-Pines, Sibel Kantarci, Brynn Levy, Michael J Macera, Fabiola Quintero-Rivera, Erica Spiegel, Blair Stevens, Janet E Ulm, Dorothy Warburton, Louise E Wilkins-Haug, Naomi Yachelevich, James F Gusella, Michael E Talkowski, Cynthia C Morton
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care...
October 5, 2016: American Journal of Human Genetics
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