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https://www.readbyqxmd.com/read/28638988/same-day-genomic-and-epigenomic-diagnosis-of-brain-tumors-using-real-time-nanopore-sequencing
#1
Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P Kloosterman, Shai Rosenberg, Mailys Daniau, Charlotte Schmitt, Julien Masliah-Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean-Yves Delattre, Ahmed Idbaih
Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making...
June 21, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28636889/complications-of-hematopoietic-stem-transplantation-fungal-infections
#2
REVIEW
Ali S Omrani, Reem S Almaghrabi
Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) are at increased risk of invasive fungal infections, especially during the early neutropenic phase and severe graft-versus-host disease. Mold-active prophylaxis should be limited to the highest risk groups. Empiric antifungal therapy for HSCT with persistent febrile neutropenia is associated with unacceptable response rates, unnecessary antifungal therapy, increased risk of toxicity, and inflated costs. Empiric therapy should not be a substitute for detailed work up to identify the cause of fever in such patients...
June 13, 2017: Hematology/oncology and Stem Cell Therapy
https://www.readbyqxmd.com/read/28630193/pyrazinamide-susceptibility-and-pnca-mutation-profile-of-mycobacterium-tuberculosis-among-multi-drug-resistant-tuberculosis-patients-in-bangladesh
#3
Arfatur Rahman, Sara Sabrina Ferdous, Shahriar Ahmed, S M Mazidur Rahman, Mohammad Khaja Mafij Uddin, Suporn Pholwat, Jean Gratz, Eric Houpt, Sayera Banu
Pyrazinamide (PZA) is a front line anti-tuberculosis (anti-TB) drug used in both first and second line treatment regimen. However, due to complex laboratory requirements, the PZA susceptibility test is rarely performed leading to the scarcity of data. Bangladesh is both a high TB and multi-drug resistant (MDR-TB) burden country but to our knowledge the published data on PZA susceptibility is limited, especially among MDR-TB patients. We aimed to analyze the PZA susceptibility pattern of Mycobacterium tuberculosis (MTB) isolates from MDR-TB patients and to correlate pncA mutation with PZA resistance in Bangladesh...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28627817/turbidimetric-determination-of-fecal-calprotectin-using-two-table-top-chemistry-analyzers-mindray-bs-200e-and-cobas%C3%A2-c111
#4
Aleksandra Mandic-Havelka, Tom Nilsen, Kathrin Sunde, Maria Norell, Lars O Hansson, Anders Larsson
BACKGROUND: Fecal calprotectin assays are widely used in diagnosis and monitoring of inflammatory bowel disease (IBD) in patients with suspected IBD. The most frequently used technique is ELISA and microtiter plates. Turbidimetric assays for analysis of fecal calprotectin can significantly reduce turnaround time. Many laboratories may be reluctant to run fecal samples on their large chemistry analyzers. The aim of this study was to evaluate fecal calprotectin particle enhanced turbidimetric immunoassay (PETIA) on smaller chemistry analyzers that could be dedicated for fecal samples...
May 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28623557/proving-value-in-radiology-experience-developing-and-implementing-a-shareable-open-source-registry-platform-driven-by-radiology-workflow
#5
Judy Wawira Gichoya, Marc D Kohli, Paul Haste, Elizabeth Mills Abigail, Matthew S Johnson
Numerous initiatives are in place to support value based care in radiology including decision support using appropriateness criteria, quality metrics like radiation dose monitoring, and efforts to improve the quality of the radiology report for consumption by referring providers. These initiatives are largely data driven. Organizations can choose to purchase proprietary registry systems, pay for software as a service solution, or deploy/build their own registry systems. Traditionally, registries are created for a single purpose like radiation dosage or specific disease tracking like diabetes registry...
June 16, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28620372/deep-sequencing-in-infectious-diseases-immune-and-pathogen-repertoires-for-the-improvement-of-patient-outcomes
#6
William F Burkholder, Evan W Newell, Michael Poidinger, Swaine Chen, Katja Fink
The inaugural workshop "Deep Sequencing in Infectious Diseases: Immune and Pathogen Repertoires for the Improvement of Patient Outcomes" was held in Singapore on 13-14 October 2016. The aim of the workshop was to discuss the latest trends in using high-throughput sequencing, bioinformatics, and allied technologies to analyze immune and pathogen repertoires and their interplay within the host, bringing together key international players in the field and Singapore-based researchers and clinician-scientists. The focus was in particular on the application of these technologies for the improvement of patient diagnosis, prognosis and treatment, and for other broad public health outcomes...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28609453/evaluation-of-a-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-assisted-selective-broth-method-to-screen-for-vancomycin-resistant-enterococci-in-patients-at-high-risk
#7
Tsi-Shu Huang, Susan Shin-Jung Lee, Chia-Chien Lee, Chiu-Yen Chen, Fang-Chen Chen, Bao-Chen Chen, Cheng Len Sy, Kuan-Sheng Wu
BACKGROUND: Bile esculin azide with vancomycin (BEAV) medium is a sensitive, but slightly less specific method for vancomycin-resistant enterococci (VRE) screening. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of clinical pathogens. This study aimed to assess the performance of a novel combination screening test for VRE, using BEAV broth combined with MALDI-TOF MS. MATERIALS AND METHODS: Clinical specimens were collected from patients at risk of VRE carriage, and tested by the novel combination method, using selective BEAV broth culture method followed by MALDI-TOF MS identification (SBEAVM)...
2017: PloS One
https://www.readbyqxmd.com/read/28586388/a-prospective-pilot-study-of-genome-wide-exome-and-transcriptome-profiling-in-patients-with-small-cell-lung-cancer-progressing-after-first-line-therapy
#8
Glen J Weiss, Sara A Byron, Jessica Aldrich, Ashish Sangal, Heather Barilla, Jeffrey A Kiefer, John D Carpten, David W Craig, Timothy G Whitsett
BACKGROUND: Small cell lung cancer (SCLC) that has progressed after first-line therapy is an aggressive disease with few effective therapeutic strategies. In this prospective study, we employed next-generation sequencing (NGS) to identify therapeutically actionable alterations to guide treatment for advanced SCLC patients. METHODS: Twelve patients with SCLC were enrolled after failing platinum-based chemotherapy. Following informed consent, genome-wide exome and RNA-sequencing was performed in a CLIA-certified, CAP-accredited environment...
2017: PloS One
https://www.readbyqxmd.com/read/28540851/from-xe-2100-to-xn-9000-from-sis-standard-to-gfhc-recommendations-for-slide-review-potential-impact-on-review-rate-and-turnaround-time
#9
Anne Tamigniau, Nicolas Bailly, Bernard Chatelain, François Mullier
In 2014, we moved from XE-2100 with Standard SIS rules to XN-9000 with GFHC recommendations for slide review. The aim of our study was to evaluate the potential impact of the new Sysmex(®) automation with implementation of GFHC rules on our review rate, turnaround time (TAT), workload and on CD34+ stem cells enumeration. We conducted a retrospective observational study from September 2013 through August 2014, in CHU Dinant Godinne UCL Namur. With the GFHC recommendations and the new Sysmex(®) automation, we significantly reduced our review rate by nearly 30% considering all units (35...
June 1, 2017: Annales de Biologie Clinique
https://www.readbyqxmd.com/read/28531259/guideline-adherence-for-diagnostic-faeces-testing-in-primary-care-patients-with-gastroenteritis
#10
Alwin Schierenberg, Berna D L Broekhuizen, Martine D Nipshagen, Maarten B J Kommer, Patricia C J Bruijning-Verhagen, Sanne van Delft, Alma C van de Pol, Marc J M Bonten, Niek J de Wit
Background.: Gastroenteritis (GE) is a common reason for primary care consultation. Dutch clinical practice guidelines (CPG) recommend diagnostic faeces testing (DFT) only in primary care patients with severe illness, comprised immunity or increased transmission risk. For its superior accuracy, shorter turnaround time and ease of use, polymerase chain reaction (PCR)-based DFT has largely replaced conventional techniques. It is unknown whether this changed CPG adherence. Objective...
May 20, 2017: Family Practice
https://www.readbyqxmd.com/read/28523416/utility-of-ct-oral-contrast-administration-in-the-emergency-department-of-a-quaternary-oncology-hospital-diagnostic-implications-turnaround-times-and-assessment-of-ed-physician-ordering
#11
Corey T Jensen, Katherine J Blair, Ott Le, Jia Sun, Wei Wei, Brinda Rao Korivi, Ajaykumar C Morani, Nicolaus A Wagner-Bartak
PURPOSE: To compare studies with and without oral contrast on performance of multidetector computed tomography (CT) and the order to CT examination turnaround time in cancer patients presenting to the emergency department (ED). To the best of our knowledge, oral contrast utility has not previously been specifically assessed in cancer patients presenting to the emergency department. MATERIALS & METHODS: Retrospective review of CT abdomen examinations performed in oncology patients presenting to the emergency department during one month...
May 18, 2017: Abdominal Radiology
https://www.readbyqxmd.com/read/28487577/nasal-swab-results-for-methicillin-resistant-staphylococcus-aureus-and-associated-infections
#12
Josée Rioux, Jenny Edwards, Lauren Bresee, Adrian Abu-Ulba, Stephen Yu, Deonne Dersch-Mills, Ben Wilson
BACKGROUND: Nasal-swab screening for methicillin-resistant Staphylococcus aureus (MRSA) has a quicker turnaround time than other bacterial culture methods, with results available within 24 h. Although MRSA nasal-swab screening is not intended to guide antimicrobial therapy, this method may give clinicians additional information for earlier tailoring of empiric antimicrobial agents. OBJECTIVE: To describe the diagnostic characteristics of nasal-swab screening in predicting MRSA infections in hospitalized patients receiving empiric treatment with IV vancomycin...
March 2017: Canadian Journal of Hospital Pharmacy
https://www.readbyqxmd.com/read/28480178/next-generation-sequencing-of-brca1-2-in-breast-cancer-patients-potential-effects-on-clinical-decision-making-using-rapid-high-accuracy-genetic-results
#13
Hyung Seok Park, Seo-Jin Park, Jee Ye Kim, Sanghwa Kim, Jaegyu Ryu, Joohyuk Sohn, Seho Park, Gun Min Kim, In Sik Hwang, Jong-Rak Choi, Seung Il Kim
PURPOSE: We evaluated the clinical role of rapid next-generation sequencing (NGS) for identifying BRCA1/2 mutations compared to traditional Sanger sequencing. METHODS: Twenty-four paired samples from 12 patients were analyzed in this prospective study to compare the performance of NGS to the Sanger method. Both NGS and Sanger sequencing were performed in 2 different laboratories using blood samples from patients with breast cancer. We then analyzed the accuracy of NGS in terms of variant calling and determining concordance rates of BRCA1/2 mutation detection...
May 2017: Annals of Surgical Treatment and Research
https://www.readbyqxmd.com/read/28479369/genomic-profiling-of-advanced-non-small-cell-lung-cancer-in-community-settings-gaps-and-opportunities
#14
Martin E Gutierrez, Kelly Choi, Richard B Lanman, Edward J Licitra, Stanley M Skrzypczak, Ruth Pe Benito, Tommy Wu, Srikesh Arunajadai, Sukhi Kaur, Harry Harper, Andrew L Pecora, Eric V Schultz, Stuart L Goldberg
BACKGROUND: National guidelines have advocated broad molecular profiling as a part of the standard diagnostic evaluation for advanced non-small cell lung cancer (NSCLC), with the goal of identifying driver mutations for which effective therapies or clinical trials are available. However, adherence to genomic testing guidelines could present challenges to community oncologists. PATIENTS AND METHODS: We performed a retrospective review of genomic testing patterns in patients with nonsquamous NSCLC treated by 89 oncologists at 15 sites throughout New Jersey and Maryland from January 2013 to December 2015...
April 13, 2017: Clinical Lung Cancer
https://www.readbyqxmd.com/read/28473040/individualized-medicine-in-gastroenterology-and-hepatology
#15
REVIEW
Michael C Stephens, Lisa A Boardman, Konstantinos N Lazaridis
After the completion of the Human Genome Project, there has been an acceleration in methodologies on sequencing nucleic acids (DNA and RNA) at a high precision and with ever-decreasing turnaround time and cost. Collectively, these approaches are termed next-generation sequencing and are already affecting the transformation of medical practice. In this symposium article, we highlight the current knowledge of the genetics of selected gastrointestinal tract and liver diseases, namely, inflammatory bowel disease, hereditary cholestatic liver disease, and familial colon cancer syndromes...
May 2017: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/28460572/next-generation-sequencing-of-pancreatic-ductal-adenocarcinoma-right-or-wrong
#16
Ashton A Connor, Steven Gallinger
Pancreatic ductal adenocarcinoma (PDAC) has the highest mortality rate of all epithelial malignancies and a paradoxically rising incidence rate. Clinical translation of next generation sequencing (NGS) of tumour and germline samples may ameliorate outcomes by identifying prognostic and predictive genomic and transcriptomic features in appreciable fractions of patients, facilitating enrolment in biomarker-matched trials. Areas covered: The literature on precision oncology is reviewed. It is found that outcomes may be improved across various malignancies, and it is suggested that current issues of adequate tissue acquisition, turnaround times, analytic expertise and clinical trial accessibility may lessen as experience accrues...
May 10, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28456989/methods-for-determination-of-%C3%AE-glycosidase-%C3%AE-glycosidase-and-%C3%AE-galactosidase-activities-in-dried-blood-spot-samples
#17
Eser Yıldırım Sozmen, Ebru Demirel Sezer
The lysosomal storage diseases (LDSs) are a heterogeneous group of inherited genetic disorders caused by defects of lysosomal proteins. The accumulation of undigested substrates from different catabolic pathways leads to cellular dysfunction. LSDs generally presents during early childhood and have a devastating impact on the families and on public health. Over the years, approaches for treatment of some LSDs have been developed with different strategies. Increasing availability of treatments of these diseases has accelerated the development of new methods and techniques for rapid diagnosis in patients with clinical indication...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28455884/two-hour-evaluation-and-referral-model-for-shorter-turnaround-times-in-the-emergency-department
#18
John A Burke, Jaimi Greenslade, Jadwiga Chabrowska, Katherine Greenslade, Sally Jones, Jacqueline Montana, Anthony Bell, Alan O'Connor
OBJECTIVE: The objective of this study was to assess the implementation of a novel ED model of care, which combines clinical streaming, team-based assessment and early senior consultation to reduce length of stay. METHODS: A pre-post-intervention study was used to compare ED performance following an extensive clinical redesign programme. Clinical teams and work sequences were reconfigured to promote the role of the staff specialist, with a focus on earlier decisions regarding disposition...
June 2017: Emergency Medicine Australasia: EMA
https://www.readbyqxmd.com/read/28450195/evaluation-of-the-eazyplex-mrsa-assay-for-the-rapid-detection-of-staphylococcus-aureus-in-pleural-and-synovial-fluid
#19
D Henares, P Brotons, X Buyse, I Latorre, H D de Paz, C Muñoz-Almagro
OBJECTIVE: Loop-mediated isothermal amplification (LAMP) is a simple and sensitive technique for rapid microbiological diagnosis. The aim of this study was to evaluate the analytical and diagnostic performance of the LAMP eazyplex MRSA test for the direct detection and differentiation of methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) in synovial/pleural fluid. METHODS: Analytical validation included the determination of the limit of detection (LoD) and analytical specificity of the eazyplex MRSA test...
April 24, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28443944/the-role-of-thromboelastometry-in-the-assessment-and-treatment-of-coagulopathy-in-liver-transplant-patients
#20
Raffael Pereira Cezar Zamper, Thiago Chaves Amorim, Luiz Guilherme Villares da Costa, Flávio Takaoka, Ary Serpa
Perioperative monitoring of coagulation is vital to assess bleeding risks, diagnose deficiencies associated with hemorrhage, and guide hemostatic therapy in major surgical procedures, such as liver transplantation. Routine static tests demand long turnaround time and do not assess platelet function; they are determined on plasma at a standard temperature of 37°C; hence these tests are ill-suited for intraoperative use. In contrast, methods which evaluate the viscoelastic properties of whole blood, such as thromboelastogram and rotational thromboelastometry, provide rapid qualitative coagulation assessment and appropriate guidance for transfusion therapy...
April 20, 2017: Einstein
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