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Molecular diagnostic methods

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https://www.readbyqxmd.com/read/28821459/clinical-multi-omics-strategies-for-the-effective-cancer-management
#1
REVIEW
Byong Chul Yoo, Kyung-Hee Kim, Sang Myung Woo, Jae Kyung Myung
Cancer is a global health issue as a multi-factorial complex disease, and early detection and novel therapeutic strategies are required for more effective cancer management. With the development of systemic analytical -omics strategies, the therapeutic approach and study of the molecular mechanisms of carcinogenesis and cancer progression have moved from hypothesis-driven targeted investigations to data-driven untargeted investigations focusing on the integrated diagnosis, treatment, and prevention of cancer in individual patients...
August 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28821190/fibromatosis-of-the-breast-diagnostic-accuracy-of-core-needle-biopsy
#2
M Gabriela Kuba, Susan C Lester, Catherine S Giess, Monica M Bertagnolli, Tad J Wieczorek, Jane E Brock
Objectives: Fibromatosis of the breast is an uncommon neoplasm with potential for local recurrence. Treatment has traditionally been surgical excision with current trends toward conservative management. Given the option of observation after diagnosis by core needle biopsy (CNB), we sought to evaluate the accuracy of CNB for diagnosing fibromatosis. Methods: We identified a total of 31 cases in which fibromatosis had been diagnosed or included in the differential diagnosis on a CNB, an excision, or both...
September 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28819248/a-portable-microfluidic-platform-for-rapid-molecular-diagnostic-testing-of-patients-with-myeloproliferative-neoplasms
#3
Hua Wang, Xinju Zhang, Xiao Xu, Qunfeng Zhang, Hengliang Wang, Dong Li, Zhihua Kang, Zhiyuan Wu, Yigui Tang, Zhenhua An, Ming Guan
The ability to simultaneously detect JAK2 V617F and MPL W515K/L mutations would substantially improve the early diagnosis of myeloproliferative neoplasms (MPNs) and decrease the risk of arterial thrombosis. The goal of this study is to achieve a point of care testing platform for simultaneous analysis of major genetic alterations in MPN. Here, we report a microfluidic platform including a glass capillary containing polypropylene matrix that extracts genomic DNA from a drop of whole blood, a microchip for simultaneous multi-gene mutation screening, and a handheld battery-powered heating device...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819114/isothermal-amplification-of-long-discrete-dna-fragments-facilitated-by-single-stranded-binding-protein
#4
Yinhua Zhang, Nathan A Tanner
Isothermal amplification methods for detection of DNA and RNA targets have expanded significantly in recent years, promising a new wave of simple and rapid molecular diagnostics. Current isothermal methods result in the generation of short fragments (<150 base pairs) or highly branched long DNA products. Here we report the amplification of discrete target fragments of several kilobases at 37 °C from both double- and single-stranded circular template DNA using specific primer pairs. In contrast to existing methods, this amplification requires only the single-stranded DNA-binding protein gp32 from bacteriophage T4 and a strand-displacing DNA polymerase...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818992/long-half-life-89-zr-labeled-radiotracers-can-guide-in-suite-percutaneous-molecular-imaging-pet-ct-guided-biopsies-without-reinjection-of-radiotracer
#5
Francois H Cornelis, Jeremy Durack, Neeta Pandit-Taskar, Gary A Ulaner, Jason S Lewis, Michael J Morris, Stephen B Solomon
Rationale: To evaluate the feasibility of in suite Zr89 labeled radiotracer positron emission tomography-computed tomography (PET/CT)-guided biopsies performed without reinjection. Methods: From 2013-2016, 12 patients (7 males, 5 females; mean age 61 years, range 40-75) with suspected metastatic prostate or breast carcinoma on either imaging or biochemical progression underwent 14 percutaneous biopsies after diagnostic PET/CT using (89)Zr labeled radiotracers (mean dose: 180MBq; range: 126-189MBq) targeting prostate specific membrane antigen (PSMA) (n = 7) or human epidermal growth factor receptor 2 (HER2) (n = 5)...
August 17, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28818623/leptospira-species-molecular-epidemiology-in-the-genomic-era
#6
K Caimi, S Repetto, V Varni, P Ruybal
Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach...
August 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28817827/role-of-next-generation-sequencing-as-a-diagnostic-tool-for-the-evaluation-of-bone-and-soft-tissue-tumors
#7
Kinga Szurian, Karl Kashofer, Bernadette Liegl-Atzwanger
Bone and soft-tissue tumors are in general rare. Diagnosing these tumors is challenging based on the significant number of different tumor entities, the rareness of these tumors, and the considerable morphological heterogeneity which can be found within a single tumor entity. Considering that more than half of the described soft-tissue tumors and approximately 25% of the bone tumors harbor recurrent genetic alterations, the use of auxiliary molecular examinations should be strongly considered. Molecular analyses are important to confirm the diagnosis, to guide treatment, to provide information about prognosis, and to allow patient recruitment for basket trials based on the molecular signature of a tumor...
August 18, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28817585/selecting-targets-for-the-diagnosis-of-schistosoma-mansoni-infection-an-integrative-approach-using-multi-omic-and-immunoinformatics-data
#8
Gardenia B F Carvalho, Daniela M Resende, Liliane M V Siqueira, Marcelo D Lopes, Débora O Lopes, Paulo Marcos Z Coelho, Andréa Teixeira-Carvalho, Jeronimo C Ruiz, Cristina T Fonseca
In order to effectively control and monitor schistosomiasis, new diagnostic methods are essential. Taking advantage of computational approaches provided by immunoinformatics and considering the availability of Schistosoma mansoni predicted proteome information, candidate antigens of schistosomiasis were selected and used in immunodiagnosis tests based on Enzime-linked Immunosorbent Assay (ELISA). The computational selection strategy was based on signal peptide prediction; low similarity to human proteins; B- and T-cell epitope prediction; location and expression in different parasite life stages within definitive host...
2017: PloS One
https://www.readbyqxmd.com/read/28815327/molecular-characterization-and-heterogeneity-of-circulating-tumor-cells-in-breast-cancer
#9
Anna Jakabova, Zuzana Bielcikova, Eliska Pospisilova, Rafal Matkowski, Bartlomiej Szynglarewicz, Urszula Staszek-Szewczyk, Milada Zemanova, Lubos Petruzelka, Petra Eliasova, Katarina Kolostova, Vladimir Bobek
INTRODUCTION: This study analyzes peripheral blood samples from breast cancer (BC) patients. CTCs from peripheral blood were enriched by size-based separation and were then cultivated in vitro. The primary aim of this study was to demonstrate the antigen independent CTC separation method with high CTC recovery. Subsequently, CTCs enriched several times during the treatment were characterized molecularly. METHODS: Patients with different stages of BC (N = 167) were included into the study...
August 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28815000/african-tick-bite-fever-in-returning-swedish-travellers-report-of-two-cases-and-aspects-of-diagnostics
#10
Kenneth Nilsson, Katarina Wallménius, Pernilla Rundlöf-Nygren, Susanne Strömdahl, Carl Påhlson
Introduction: African tick-bite fever, caused by Rickettsia africae, is endemic in rural areas of sub-Saharan Africa and a possible cause of fever in returning Swedish travellers. Two patients are presented, and the advantages and disadvantages of different diagnostic methods are discussed. Patients and methods: Two middle-aged men fell ill with fever after returning home from South Africa. Both had single eschars and one also presented with a lymph node swelling. Samples were taken for serology, general bacterial culture from the wound (Patient 1) using a swab and additionally for Patient 2 PCR of a skin biopsy from the eschar...
2017: Infection Ecology & Epidemiology
https://www.readbyqxmd.com/read/28814156/a-method-to-compare-the-performance-of-two-molecular-diagnostic-tools-in-the-absence-of-a-gold-standard
#11
Xiaonan Xue, Maja Oktay, Sumanta Goswami, Mimi Y Kim
The paper is motivated by the problem of comparing the accuracy of two molecular tests in detecting genetic mutations in tumor samples when there is no gold standard test. Commonly used sequencing methods require a large number of tumor cells in the tumor sample and the proportion of tumor cells with mutation positivity to be above a threshold level whereas new tests aim to reduce the requirement for number of tumor cells and the threshold level. A new latent class model is proposed to compare these two tests in which a random variable is used to represent the unobserved proportion of mutation positivity so that these two tests are conditionally dependent; furthermore, an independent random variable is included to address measurement error associated with the reading from each test, while existing latent class models often assume conditional independence and do not allow measurement error...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28811535/delimiting-species-of-protaphorura-collembola-onychiuridae-integrative-evidence-based-on-morphology-dna-sequences-and-geography
#12
Xin Sun, Feng Zhang, Yinhuan Ding, Thomas W Davies, Yu Li, Donghui Wu
Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807308/presence-and-species-identity-of-rumen-flukes-in-cattle-and-sheep-in-the-netherlands
#13
H W Ploeger, L Ankum, L Moll, D C K van Doorn, G Mitchell, P J Skuce, R N Zadoks, M Holzhauer
The purpose of the study was to gain knowledge about the prevalence and identity of rumen flukes (RF) in cattle and sheep in the Netherlands. Routine faecal examinations of diagnostic submissions between May 2009 and September 2014 showed a mean annual herd or flock RF prevalence of 15.8% for cattle and 8.0% for sheep. Prevalence in cattle was higher after 2012 than before, which may reflect a change in detection method as well as an increase in true prevalence. During November and December 2014, an abattoir survey was conducted to allow for scoring of rumen fluke burden and to obtain specimens for molecular species characterization...
August 30, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28805633/of-phlebotomines-sandflies-and-viruses-a-comprehensive-perspective-on-a-complex-situation
#14
REVIEW
Nazli Ayhan, Remi N Charrel
Old World sandfly-borne phleboviruses are classified into three serological complexes: Sandfly fever Sicilian, Sandfly fever Naples and Salehabad. Human pathogens (febrile illness ['sandfly fever'], neuroinvasive infections) belong to the two first complexes. The increasing number of newly discovered sandfly-borne phleboviruses raises concerns about their medical and veterinary importance. They occupy a wide geographic area from Mediterranean basin to North Africa and the Middle East to the central Asia. At least nine species of sandflies can transmit these viruses...
August 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28804563/count-based-size-correction-analysis-of-maternal-plasma-dna-for-improved-noninvasive-prenatal-detection-of-fetal-trisomies-13-18-and-21
#15
Li Zhang, Qian Zhu, He Wang, Shanling Liu
PURPOSE: Our goal was to derive more sensitive and accurate Z-scores based on combined DNA count- and size-based algorithms to advance molecular diagnostics for noninvasive prenatal testing of fetal trisomies. METHODS: We included 180 cases at high risk for fetal aneuploidy who underwent amniotic fluid cytogenetic analysis. We calculated their traditional count-based Z-scores, as well as their 100-, 130- and 150-, and 166-bp size-corrected Z-scores, and determined each Z-score's reliability based on its comparison to the cases' cytogenetic results...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28802405/detection-of-mycobacterium-tuberculosis-from-paraffin-embedded-tissues-by-genexpert-mtb-rif
#16
Laura Rindi, Greta Alì, Barbara Fabiani, Gabriella Fontanini, Carlo Garzelli
GeneXpert MTB/RIF (Xpert) assay, a rapid and automated system based on real-time PCR and molecular beacon technology, proved to be a sensitive and specific tool capable of detecting Mycobacterium tuberculosis and rifampin resistance in clinical specimens. In this study we provide a Xpert-dedicated successful protocol for processing paraffin-embedded tissue and assess the feasibility of the Xpert assay-based tuberculosis (TB) diagnosis on these specimens, thus proving the Xpert assay as a valuable TB diagnostic tool in supporting conventional histopathological methods...
September 2017: Tuberculosis
https://www.readbyqxmd.com/read/28801929/validation-and-application-of-a-novel-integrated-genetic-screening-method-to-a-cohort-of-1-112-men-with-idiopathic-azoospermia-or-severe-oligozoospermia
#17
Manon S Oud, Liliana Ramos, Moira K O'Bryan, Robert I McLachlan, Özlem Okutman, Stephane Viville, Petra F de Vries, Dominique F C M Smeets, Dorien Lugtenberg, Jayne Y Hehir-Kwa, Christian Gilissen, Maartje van de Vorst, Lisenka E L M Vissers, Alexander Hoischen, Aukje M Meijerink, Kathrin Fleischer, Joris A Veltman, Michiel J Noordam
Microdeletions of the Y chromosome (YCMs), Klinefelter syndrome (47,XXY) and CFTR mutations are known genetic causes of severe male infertility, but the majority of cases remain idiopathic. Here we describe a novel method using single molecule Molecular Inversion Probes (smMIPs), to screen infertile men for mutations and copy number variations (CNVs) affecting known disease genes. We designed a set of 4,525 smMIPs targeting the coding regions of causal (n = 6) and candidate (n = 101) male infertility genes...
August 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28800730/genotypes-of-hepatitis-a-virus-in-turkey-first-report-and-clinical-profile-of-children-infected-with-sub-genotypes-ia-and-iiia
#18
Huseyin Yilmaz, Asiye Karakullukcu, Nuri Turan, Utku Y Cizmecigil, Aysun Yilmaz, Ayse A Ozkul, Ozge Aydin, Alper Gunduz, Mahmut Mete, Fadile Y Zeyrek, Taner T Kirazoglu, Juergen A Richt, Bekir Kocazeybek
BACKGROUND: Hepatitis A virus (HAV) is a food and water-borne virus causing clinical (mainly hepatitis) and subclinical disease in humans. It is important to characterize circulating strains of HAV in order to prevent HAV infections using efficacious vaccines. The aim of this study was the detection and characterization of the circulating strains of HAV in Turkey by performing serology, RT-PCR, sequencing and phylogenetic analysis. METHODS: In this study, 355 HAV suspected cases were analysed by ELISA for the presence of antibodies to HAV...
August 11, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28798845/vancomycin-resistant-gene-identification-from-live-bacteria-on-an-integrated-microfluidic-system-by-using-low-temperature-lysis-and-loop-mediated-isothermal-amplification
#19
Wen-Hsin Chang, Ju-Ching Yu, Sung-Yi Yang, Yi-Cheng Lin, Chih-Hung Wang, Huey-Ling You, Jiunn-Jong Wu, Mel S Lee, Gwo-Bin Lee
Vancomycin-resistant Enterococcus (VRE) is a kind of enterococci, which shows resistance toward antibiotics. It may last for a long period of time and meanwhile transmit the vancomycin-resistant gene (vanA) to other bacteria. In the United States alone, the resistant rate of Enterococcus to vancomycin increased from a mere 0.3% to a whopping 40% in the past two decades. Therefore, timely diagnosis and control of VRE is of great need so that clinicians can prevent patients from becoming infected. Nowadays, VRE is diagnosed by antibiotic susceptibility test or molecular diagnosis assays such as matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and polymerase chain reaction...
March 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28797494/laboratory-diagnostics-for-fungal-infections-a-review-of-current-and-future-diagnostic-assays
#20
REVIEW
Poornima Ramanan, Nancy L Wengenack, Elitza S Theel
This article reviews the current diagnostic approaches, both serologic and molecular, for the detection of fungi associated with pulmonary disease. Classic serologic techniques, including immunodiffusion and complement fixation, both of which remain a cornerstone for fungal diagnostic testing, are reviewed and their performance characteristics presented. More recent advances in this field, including novel lateral-flow assays for fungal antigen detection, are also described. Molecular techniques for fungal identification both from culture and directly from patient specimens, including nucleic acid probes, mass spectrometry-based methods, nucleic acid amplification testing, and traditional and broad-range sequencing, are discussed and their performance evaluated...
September 2017: Clinics in Chest Medicine
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