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https://www.readbyqxmd.com/read/28228113/validation-of-an-ngs-mutation-detection-panel-for-melanoma
#1
Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead, Ian A Cree
BACKGROUND: Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. METHODS: While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time...
February 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28222757/spatiotemporal-dynamics-of-hiv-1-transmission-in-france-1999-2014-and-impact-of-targeted-prevention-strategies
#2
Antoine Chaillon, Asma Essat, Pierre Frange, Davey M Smith, Constance Delaugerre, Francis Barin, Jade Ghosn, Gilles Pialoux, Olivier Robineau, Christine Rouzioux, Cécile Goujard, Laurence Meyer, Marie-Laure Chaix
BACKGROUND: Characterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort over 15 years. RESULTS: Sociodemographic, geographic, clinical, biological and pol sequence data from 1356 patients were collected between 1999 and 2014. Network analysis was performed to infer genetic relationships, i...
February 21, 2017: Retrovirology
https://www.readbyqxmd.com/read/28222600/a-rapid-immunoassay-for-detection-of-infliximab-in-whole-blood-using-a-fiber-optic-spr-biosensor
#3
Jiadi Lu, Dragana Spasic, Filip Delport, Thomas Van Stappen, Iris Detrez, Devin Daems, Séverine Vermeire, Ann Gils, Jeroen Lammertyn
Monitoring the concentration of a therapeutic drug antibody, infliximab (IFX), is recommended for enhancing its efficacy in patients with inflammatory bowel disease (IBD). However, IFX concentrations are currently determined in patients' serum/plasma, which requires sample preparation from blood, hence hampering the turnaround time. In this paper, we present a short immunoassay (10 minutes) using fiber-optic SPR (FO-SPR) biosensor for detection of IFX spiked in 100-fold diluted serum, plasma and whole blood...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28222019/practical-motives-are-prominent-in-test-ordering-in-the-emergency-department
#4
Armando van der Horst, Dennis J van de Wijngaart, Jolanda Scherrenburg, Nadine van Dijk, Pim M W Janssens
BACKGROUND: Laboratory test ordering under time pressure may impact test-ordering behavior. METHODS: To investigate the test-ordering behavior of doctors working under such pressure, we designed a questionnaire for trainees and staff in the Emergency Department (ED). This questionnaire addressed topics such as necessity of requested tests, time spent on ordering, costs and availability of tests, and the time of the day. We hypothesized that ordering behavior would be guided predominantly by the medical need of tests and aimed at identifying practical motives that also have an effect...
February 21, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28213382/pharmacist-involvement-on-a-rapid-response-team
#5
Joel Feih, William J Peppard, Michael Katz
PURPOSE: The effect of a pharmacist on a rapid response team (RRT) was investigated. METHODS: This study evaluated 234 patients before and 157 patients after pharmacist involvement on an RRT. The primary outcome was time to medication administration, with a goal turnaround time of less than 30 minutes. Secondary outcomes included most frequently used medications, readmissions to the intensive care unit (ICU) within 48 hours, number of rapid responses that resulted in ICU admission, length of hospital stay, and survival to hospital discharge...
March 1, 2017: American Journal of Health-system Pharmacy: AJHP
https://www.readbyqxmd.com/read/28207411/reporting-altered-test-results-in-hemolyzed-samples-is-the-cure-worse-than-the-disease
#6
Giuseppe Lippi, Gianfranco Cervellin, Mario Plebani
The management of laboratory data in unsuitable (hemolyzed) samples remains an almost unresolved dilemma. Whether or not laboratory test results obtained by measuring unsuitable specimens should be made available to the clinicians has been the matter of fierce debates over the past decades. Recently, an intriguing alternative to suppressing test results and recollecting the specimen has been put forward, entailing the definition and implementation of specific algorithms that would finally allow reporting a preanalytically altered laboratory value within a specific comment about its uncertainty of measurement...
February 16, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28203570/multifocal-gastric-ulcers-caused-by-diffuse-large-b-cell-lymphoma-in-a-patient-with-significant-weight-loss
#7
Mark A Gromski, Jennifer L Peng, Jiehao Zhou, Howard C Masuoka, Attaya Suvannasankha, Suthat Liangpunsakul
Primary gastrointestinal (GI) lymphoma is a heterogeneous disease with varied clinical presentations. The stomach is the most common GI site and accounts for 70% to 75% of GI lymphomas. We present a patient with gastric diffuse large B cell lymphoma (DLBCL) who presented with significant weight loss, early satiety, and multifocal ulcerated gastric lesions. Esophagoduodenoscopy should be performed in patients presenting with warning symptoms as in our case. Diagnosis is usually made by endoscopic biopsies. Multiple treatment modalities including surgery, radiotherapy, and chemotherapy have been used...
October 2016: Journal of Investigative Medicine High Impact Case Reports
https://www.readbyqxmd.com/read/28201998/clinical-performance-evaluation-of-a-sensitive-rapid-low-throughput-test-for-kras-mutation-analysis-using-formalin-fixed-paraffin-embedded-tissue-samples
#8
Christine Weyn, Sofie Van Raemdonck, Robina Dendooven, Vincent Maes, Karen Zwaenepoel, Suzan Lambin, Patrick Pauwels
BACKGROUND: Testing for KRAS mutations in metastatic colorectal cancer (mCRC) on formalin-fixed, paraffin embedded (FFPE) tumor tissue has become standard of care. Different molecular methods exist to determine hotspot KRAS mutations in exon 2, 3 and 4, but testing is often limited by the sensitivity and the speed of analysis. The aim of this retrospective study was to establish the clinical performance of the Idylla™ KRAS Mutation Test on FFPE tumor samples of patients with mCRC. METHODS: KRAS mutation analysis was performed using the therascreen KRAS on the RotorGene Q platform (CE-IVD; Qiagen) and results were subsequently compared to the Idylla™ KRAS Mutation Test...
February 16, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28197949/the-impact-of-next-generation-sequencing-on-the-diagnosis-and-treatment-of-epilepsy-in-paediatric-patients
#9
REVIEW
Davide Mei, Elena Parrini, Carla Marini, Renzo Guerrini
Next-generation sequencing (NGS) has contributed to the identification of many monogenic epilepsy syndromes and is favouring earlier and more accurate diagnosis in a subset of paediatric patients with epilepsy. The cumulative information emerging from NGS studies is rapidly changing our comprehension of the relations between early-onset severe epilepsy and the associated neurological impairment, progressively delineating specific entities previously gathered under the umbrella definition of epileptic encephalopathies, thereby influencing treatment choices and limiting the most aggressive drug regimens only to those conditions that are likely to actually benefit from them...
February 14, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28196074/clinical-applicability-and-cost-of-a-46-gene-panel-for-genomic-analysis-of-solid-tumours-retrospective-validation-and-prospective-audit-in-the-uk-national-health-service
#10
Angela Hamblin, Sarah Wordsworth, Jilles M Fermont, Suzanne Page, Kulvinder Kaur, Carme Camps, Pamela Kaisaki, Avinash Gupta, Denis Talbot, Mark Middleton, Shirley Henderson, Anthony Cutts, Dimitrios V Vavoulis, Nick Housby, Ian Tomlinson, Jenny C Taylor, Anna Schuh
BACKGROUND: Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing...
February 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28193118/validation-of-polymerase-chain-reaction-based-assay-to-detect-actual-number-of-cgg-repeats-in-fmr1-gene-in-indian-fragile-x-syndrome-patients
#11
Madhumita Roy Chowdhury, Sandeepa Chauhan, Anjali Dabral, B K Thelma, Neerja Gupta, Madhulika Kabra
Molecular genetic testing for fragile X (FX) is complicated due to the large variation in the size of CGG expansion. The aim of this study was to apply this new technique using AmplideX FMR1 PCR assay, which is considered a better diagnostic tool for detecting expanded alleles in Indian population. The primary objective was to identify the carrier status of females and to correlate the instability of premutation alleles in females with the repeat sizes. 24 children with FX based on rapid PCR and 29 female relatives of these patients were included...
March 2017: Journal of Child Neurology
https://www.readbyqxmd.com/read/28166743/molecular-point-of-care-testing-for-respiratory-viruses-versus-routine-clinical-care-in-adults-with-acute-respiratory-illness-presenting-to-secondary-care-a-pragmatic-randomised-controlled-trial-protocol-respoc
#12
Nathan J Brendish, Ahalya K Malachira, Tristan W Clark
BACKGROUND: Respiratory viruses are associated with a huge socio-economic burden and are responsible for a large proportion of acute respiratory illness in hospitalised adults. Laboratory PCR is accurate but takes at least 24 h to generate a result to clinicians and antigen-based point-of-care tests (POCT) lack sensitivity. Rapid molecular platforms, such as the FilmArray Respiratory Panel, have equivalent diagnostic accuracy to laboratory PCR and can generate a result in 1 h making them deployable as POCT...
February 6, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28165299/molecular-biomarkers-for-the-evaluation-of-colorectal-cancer-guideline-from-the-american-society-for-clinical-pathology-college-of-american-pathologists-association-for-molecular-pathology-and-the-american-society-of-clinical-oncology
#13
Antonia R Sepulveda, Stanley R Hamilton, Carmen J Allegra, Wayne Grody, Allison M Cushman-Vokoun, William K Funkhouser, Scott E Kopetz, Christopher Lieu, Noralane M Lindor, Bruce D Minsky, Federico A Monzon, Daniel J Sargent, Veena M Singh, Joseph Willis, Jennifer Clark, Carol Colasacco, R Bryan Rumble, Robyn Temple-Smolkin, Christina B Ventura, Jan A Nowak
Purpose Molecular testing of colorectal cancers (CRCs) to improve patient care and outcomes of targeted and conventional therapies has been the center of many recent studies, including clinical trials. Evidence-based recommendations for the molecular testing of CRC tissues to guide epidermal growth factor receptor (EGFR) -targeted therapies and conventional chemotherapy regimens are warranted in clinical practice. The purpose of this guideline is to develop evidence-based recommendations to help establish standard molecular biomarker testing for CRC through a systematic review of the literature...
February 6, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28161563/single-center-experience-with-a-targeted-next-generation-sequencing-assay-for-assessment-of-relevant-somatic-alterations-in-solid-tumors
#14
Aino Paasinen-Sohns, Viktor H Koelzer, Angela Frank, Julian Schafroth, Aline Gisler, Melanie Sachs, Anne Graber, Sacha I Rothschild, Andreas Wicki, Gieri Cathomas, Kirsten D Mertz
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material...
February 2, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28160876/neurology-individualized-medicine-when-to-use-next-generation-sequencing-panels
#15
REVIEW
Christopher J Klein, Tatiana M Foroud
Next-generation sequencing (NGS) is increasingly being applied to clinical testing. This practice is predicted to grow especially in neurology clinics because many of their patients have monogenetic causes for their "diagnostic odyssey." The cost of sequencing has been steadily decreasing, but the cost of DNA sequencing is a minor part of the total cost. Downstream data analysis, storage, and interpretation account for most of the total expense. In patients with nonspecific neurologic disorders in which an extensive number of genetic differential diagnoses exist, whole-genome sequencing (WGS) or whole-exome sequencing (WES) has shown promise in the identification of genetic causes...
February 2017: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/28160728/point-of-care-testing-poct-in-molecular-diagnostics-performance-evaluation-of-genexpert-hcv-rna-test-in-diagnosing-and-monitoring-of-hcv-infection
#16
Ekta Gupta, Pragya Agarwala, Guresh Kumar, Rakhi Maiwall, Shiv Kumar Sarin
BACKGROUND: Molecular testing at the point-of-care may turn out to be game changer for HCV diagnosis and treatment monitoring, through increased sensitivity, reduced turnaround time, and ease of performance. One such assay GeneXpert(®) has recently been released. OBJECTIVES: Comparative analysis between performances of GeneXpert(®) and Abbott HCV-RNA was done. STUDY DESIGN: 174 HCV infected patients were recruited and, one time plasma samples from 154 patients and repeated samples from 20 patients, obtained at specific treatment time-points (0, 4, 12 and 24) weeks were serially re-tested on Xpert(®)...
March 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28152819/electronic-operative-reports-to-support-quality-improvement-and-patient-centered-care
#17
Elaine Maloney, Mary Agent-Katwala, Geoff Porter
: 95 Background: Operative reports (OP) for cancer surgery are usually narrated, although they provide inconsistent and incomplete information for patient care. National standards for cancer OP were unavailable until 2007. Over 10 years, surgeons in four Canadian provinces have transitioned from narrative to electronic synoptic reporting (ESP) for specific cancers. The electronic OP are now considered a patient medical record and integral to subsequent patient care. Surgeons are using electronic reports for quality assurance, billing, medical-legal conflict resolution and research...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28152811/successful-completion-of-egfr-alk-testing-in-non-squamous-non-small-cell-lung-cancer-non-sq-nsclc-with-the-implementation-of-reflex-testing-rt-by-pathologists
#18
Zoe Winterton-Perks, Simon Raphael, Susanna Y Cheng, Sunil Verma, Ryan Freedman, Nevkeet Toor, Joseph Perera, Matthew Anaka, Charles Victor, Parneet Kaur Cheema
: 93 Background: EGFR mutation and ALK rearrangement testing is standard in the management of advanced non-sq NSCLC patients (pts). Previously at our centre, EGFR/ALK biomarker testing was requested by medical oncologists (MO). In June 2013 we implemented biomarker RT, defined as pathologists requesting EGFR/ALK at time of diagnosis of non sq-NSCLC irrespective of stage. The objective of this study was to test the hypothesis that if pathologists requested biomarker testing, appropriate tissue would be preserved and selected for testing, which would improve success rates of biomarker testing...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28152808/ambulatory-redesign-strategies-for-quality-improvement-in-patient-care
#19
Catherine A Lyons, Nancy Smith, Maureen McGlennon, Terri L Parker, Carolyn Truini, Maureen Major-Campos, Jill Lacy, Karen Michaels, Vanna Dest, Richard Lisitano, Kerin B Adelson, Rogerio Lilenbaum
: 85 Background: Growing outpatient volume poses patient flow challenges, making it difficult to accommodate the complexities of academic medical practice. Volume increases create operational inefficiencies like delays in lab turnaround time (TAT) and limited rooming capacity resulting in delays in patient access and reduced provider productivity. These bottlenecks negatively impact patient satisfaction. METHODS: Four multidisciplinary teams assessed barriers to patient flow in the lab, rooming and scheduling process...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28138088/multi-center-evaluation-of-the-automated-immunohematology-instrument-the-ortho-vision-analyzer
#20
Agnes Aysola, Leslie Wheeler, Richard Brown, Rebecca Denham, Connie Colavecchia, Katerina Pavenski, Elizabeth Krok, Chelsea Hayes, Ellen Klapper
BACKGROUND: ORTHO VISION Analyzer (Vision), is an immunohematology instrument using ID-MT gel card technology with digital image processing. It has a continuous, random sample access with STAT priority processing. The efficiency and ease of operation of Vision was evaluated at 5 medical centers. METHODS: De-identified patient samples were tested on the ORTHO ProVue Analyzer (ProVue) and repeated on the Vision mimicking the daily workload pattern. Turnaround times (TAT) were collected and compared...
February 2017: Laboratory Medicine
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