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https://www.readbyqxmd.com/read/28725028/detection-and-quantitation-of-copy-number-variation-in-the-voltage-gated-sodium-channel-gene-of-the-mosquito-culex-quinquefasciatus
#1
Walter Fabricio Silva Martins, Krishanthi Subramaniam, Keith Steen, Henry Mawejje, Triantafillos Liloglou, Martin James Donnelly, Craig Stephen Wilding
Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28722675/using-droplet-digital-pcr-to-analyze-mycn-and-alk-copy-number-in-plasma-from-patients-with-neuroblastoma
#2
Marco Lodrini, Annika Sprüssel, Kathy Astrahantseff, Daniela Tiburtius, Robert Konschak, Holger N Lode, Matthias Fischer, Ulrich Keilholz, Angelika Eggert, Hedwig E Deubzer
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28714429/structural-brain-correlations-of-visuospatial-and-visuoperceptual-tests-in-parkinson-s-disease
#3
Anna Isabel Garcia-Diaz, Barbara Segura, Hugo Cesar Baggio, Maria Jose Marti, Francesc Valldeoriola, Yaroslau Compta, Nuria Bargallo, Carme Uribe, Anna Campabadal, Alexandra Abos, Carme Junque
BACKGROUND: Diagnosis of mild cognitive impairment in Parkinson's disease (PD) is relevant because it is a marker for evolution to dementia. However, the selection of suitable tests to evaluate separate cognitive domains in mild cognitive impairment related to PD remains an open question. The current work aims to investigate the neuroanatomical correlates of several visuospatial/visuoperceptual tests using the same sample and a multimodal MRI approach. METHODS: The study included 36 PD patients and 20 healthy subjects matched for age, sex, and education...
July 17, 2017: Journal of the International Neuropsychological Society: JINS
https://www.readbyqxmd.com/read/28711173/presymptomatic-diagnosis-of-spinal-muscular-atrophy-through-newborn-screening
#4
Yin-Hsiu Chien, Shu-Chuan Chiang, Wen-Chin Weng, Ni-Chung Lee, Ching-Jie Lin, Wu-Shiun Hsieh, Wang-Tso Lee, Yuh-Jyh Jong, Tsang-Ming Ko, Wuh-Liang Hwu
OBJECTIVE: To demonstrate the feasibility of presymptomatic diagnosis of spinal muscular atrophy (SMA) through newborn screening (NBS). STUDY DESIGN: We performed a screening trial to assess all newborns who underwent routine newborn metabolic screening at the National Taiwan University Hospital newborn screening center between November 2014 and September 2016. A real-time polymerase chain reaction (RT-PCR) genotyping assay for the SMN1/SMN2 intron 7 c.888+100A/G polymorphism was performed to detect homozygous SMN1 deletion using dried blood spot (DBS) samples...
July 12, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28694015/predicting-treatment-resistance-and-relapse-through-circulating-dna
#5
Emma Beddowes, Stephen J Sammut, Meiling Gao, Carlos Caldas
The use of circulating DNA(ctDNA) to provide a non-invasive, personalised genomic snapshot of a patients' tumour has huge potential. Over the past five years this area of research has gained huge momentum. A number of studies in metastatic breast cancer have shown the potential of ctDNA to predict prognosis and treatment response using ctDNA. Further developments have included deeper sequencing using whole exome and shallow whole genome approaches which has the potential to identify new mutations and chromosomal copy number changes which appear upon resistance to treatment...
July 7, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/28691390/an-improved-digital-polymerase-chain-reaction-protocol-to-capture-low-copy-kras-mutations-in-plasma-cell-free-dna-by-resolving-subsampling-issues
#6
REVIEW
Yusuke Ono, Ayumu Sugitani, Hidenori Karasaki, Munehiko Ogata, Reo Nozaki, Junpei Sasajima, Tomoki Yokochi, Shingo Asahara, Kazuya Koizumi, Kiyohiro Ando, Katsunori Hironaka, Tsutomu Daito, Yusuke Mizukami
Genetic alterations responsible for the initiation of cancer may serve as immediate biomarkers for early diagnosis. Plasma levels of cell-free DNA (cfDNA) in cancer patients are higher than those in healthy individuals, however, the major technical challenge for the widespread implementation of cfDNA genotyping as a diagnostic tool is the insufficient sensitivity and specificity of detecting early-stage tumors that shed low amounts of cfDNA. To establish a protocol for ultrasensitive droplet digital polymerase chain reaction (ddPCR) for quantification of low-frequency alleles within a limited cfDNA pool, two-step multiplex ddPCR targeting eight clinically relevant mutant KRAS variants was examined...
July 10, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28683077/dna-isolation-protocol-effects-on-nuclear-dna-analysis-by-microarrays-droplet-digital-pcr-and-whole-genome-sequencing-and-on-mitochondrial-dna-copy-number-estimation
#7
Elizabeth Nacheva, Katya Mokretar, Aynur Soenmez, Alan M Pittman, Colin Grace, Roberto Valli, Ayesha Ejaz, Selina Vattathil, Emanuela Maserati, Henry Houlden, Jan-Willem Taanman, Anthony H Schapira, Christos Proukakis
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol...
2017: PloS One
https://www.readbyqxmd.com/read/28673857/development-and-application-of-a-reverse-transcriptase-droplet-digital-pcr-rt-ddpcr-for-sensitive-and-rapid-detection-of-japanese-encephalitis-virus
#8
Xulong Wu, Hua Lin, Shijie Chen, Lu Xiao, Miao Yang, Wei An, Yin Wang, Xueping Yao, Zexiao Yang
Japanese encephalitis (JE) is one of the most common zoonoses caused by Japanese encephalitis virus (JEV). Droplet digital PCR (ddPCR) is a novel sensitive, accurate method that enables absolute quantitation without the need for calibration curves. The aim of this study was to develop a RT-ddPCR method to detect JEV, and to compare its sensitivity with real-time TaqMan RT-PCR by analysis of clinical samples. The methods of JEV real-time RT-PCR and RT-ddPCR were established and optimal reaction conditions were confirmed...
June 30, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28670746/hpv-circulating-tumor-dna-to-monitor-the-efficacy-of-anti-pd-1-therapy-in-metastatic-squamous-cell-carcinoma-of-the-anal-canal-a-case-report
#9
Luc Cabel, François-Clément Bidard, Vincent Servois, Wulfran Cacheux, Pascale Mariani, Emanuela Romano, Mathieu Minsat, Ivan Bieche, Fereshteh Farkhondeh, Emmanuelle Jeannot, Bruno Buecher
Squamous cell carcinoma of the anal canal (SCCA) is a rare HPV-associated cancer with limited sensitivity to standard chemotherapy. In a phase 2 study, nivolumab, an anti PD-1 immune checkpoint inhibitor, demonstrated significant efficacy as single-agent therapy in metastatic SCCA patients. Nevertheless, imaging assessment by standard RECIST criteria of the efficacy of immune therapy can be difficult in some patients due to tumor immune cell infiltration, and biomarkers of treatment efficacy are needed. We have previously developed a quantitative droplet digital PCR (ddPCR) technique to detect HPV circulating tumor DNA (HPV ctDNA), with excellent sensitivity and specificity...
July 3, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28667577/the-role-of-beaming-and-digital-pcr-for-multiplexed-analysis-in-molecular-oncology-in-the-era-of-next-generation-sequencing
#10
Jérôme Alexandre Denis, Erell Guillerm, Florence Coulet, Annette K Larsen, Jean-Marc Lacorte
BEAMing polymerase chain reaction (PCR) and digital PCR (dPCR) are used for robust and accurate quantification of nucleic acids. These methods are particularly well suited for the identification of very small fractions (<1%) of variant copies such as the presence of mutant genes in a predominantly wild-type background. BEAMing and dPCR are increasingly used in diverse fields including bacteriology, virology, non-invasive prenatal testing, and oncology, in particular for the molecular analysis of liquid biopsies...
June 30, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28665055/plagiarism-in-the-context-of-education-and-evolving-detection-strategies
#11
REVIEW
Armen Yuri Gasparyan, Bekaidar Nurmashev, Bakhytzhan Seksenbayev, Vladimir I Trukhachev, Elena I Kostyukova, George D Kitas
Plagiarism may take place in any scientific journals despite currently employed anti-plagiarism tools. The absence of widely acceptable definitions of research misconduct and reliance solely on similarity checks do not allow journal editors to prevent most complex cases of recycling of scientific information and wasteful, or 'predatory,' publishing. This article analyses Scopus-based publication activity and evidence on poor writing, lack of related training, emerging anti-plagiarism strategies, and new forms of massive wasting of resources by publishing largely recycled items, which evade the 'red flags' of similarity checks...
August 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/28656489/detection-of-brca1-gross-rearrangements-by-droplet-digital-pcr
#12
Elena V Preobrazhenskaya, Ilya V Bizin, Ekatherina Sh Kuligina, Alla Yu Shleykina, Evgeny N Suspitsin, Olga A Zaytseva, Elena I Anisimova, Sergey A Laptiev, Tatiana V Gorodnova, Alexey M Belyaev, Evgeny N Imyanitov, Anna P Sokolenko
PURPOSE: Large genomic rearrangements (LGRs) constitute a significant share of pathogenic BRCA1 mutations. Multiplex ligation-dependent probe amplification (MLPA) is a leading method for LGR detection; however, it is entirely based on the use of commercial kits, includes relatively time-consuming hybridization step, and is not convenient for large-scale screening of recurrent LGRs. MATERIALS AND METHODS: We developed and validated the droplet digital PCR (ddPCR) assay, which covers the entire coding region of BRCA1 gene and is capable to precisely quantitate the copy number for each exon...
June 27, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28654634/emergence-of-met-hyper-amplification-at-progression-to-met-and-braf-inhibition-in-colorectal-cancer
#13
Daniele Oddo, Giulia Siravegna, Annunziata Gloghini, Claudio Vernieri, Benedetta Mussolin, Federica Morano, Giovanni Crisafulli, Rosa Berenato, Giorgio Corti, Chiara Costanza Volpi, Michela Buscarino, Monica Niger, Philip D Dunne, Giuseppe Rospo, Emanuele Valtorta, Alice Bartolini, Giovanni Fucà, Simona Lamba, Antonia Martinetti, Maria Di Bartolomeo, Filippo de Braud, Alberto Bardelli, Filippo Pietrantonio, Federica Di Nicolantonio
BACKGROUND: Combined MET and BRAF inhibition showed clinical benefit in a patient with rectal cancer carrying BRAF(V600E) and MET amplification. However after 4 months, acquired resistance emerged and the patient deceased shortly after disease progression. The mechanism of resistance to this drug combination is unknown. METHODS: We analysed plasma circulating tumour DNA obtained at progression by exome sequencing and digital PCR. MET gene and mRNA in situ hybridisation analyses in two bioptic specimens obtained at progression were used to confirm the plasma data...
June 27, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28652445/increased-copy-number-variation-of-mtdna-in-an-array-based-digital-pcr-assay-predicts-ulcerative-colitis-associated-colorectal-cancer
#14
Toshiaki Tanaka, Takashi Kobunai, Yoko Yamamoto, Koji Murono, Kensuke Otani, Koji Yasuda, Takeshi Nishikawa, Tomomichi Kiyomatsu, Kazushige Kawai, Keisuke Hata, Hiroaki Nozawa, Soichiro Ishihara, Toshiaki Watanabe
AIM: Mitochondrial dysfunction plays a central role in carcinogenesis in numerous cancer-related diseases. We examined the copy number variation of mitochondrial DNA (mtDNA) and the expression of energy-producing genes in relation to ulcerative colitis (UC)-associated carcinogenesis. MATERIALS AND METHODS: We studied 17 patients with UC-associated adenocarcinoma (UC-Ca) and 16 without UC-associated adenocarcinoma (UC-nonCa). The copy number of mtDNA in non-dysplastic mucosa in both groups was quantified by an array-based digital polymerase chain reaction (PCR) assay...
July 2017: In Vivo
https://www.readbyqxmd.com/read/28642185/place-of-3d-printing-in-facial-epithesis
#15
J T Bachelet, R Jouan, V Prade, C Francisco, P Jaby, A Gleizal
Facial rehabilitation from facial epithets is part of the facial surgeon's therapeutic arsenal. The primary technique requires taking imprints on the patient, which has major drawbacks such as discomfort and difficulties for precisely recording anatomical surfaces. In this paper, we present a technical improvement in the design of facial epithesis, introducing application of a 3D printing technology. By exploiting digital data in DICOM format, it is possible to produce a digital copy of an epithesis. Based on this copy a model can be printed and then used to support the final prosthesis...
June 19, 2017: Journal of Stomatology, Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/28640831/ribosomal-dna-copy-number-loss-and-sequence-variation-in-cancer
#16
Baoshan Xu, Hua Li, John M Perry, Vijay Pratap Singh, Jay Unruh, Zulin Yu, Musinu Zakari, William McDowell, Linheng Li, Jennifer L Gerton
Ribosomal DNA is one of the most variable regions in the human genome with respect to copy number. Despite the importance of rDNA for cellular function, we know virtually nothing about what governs its copy number, stability, and sequence in the mammalian genome due to challenges associated with mapping and analysis. We applied computational and droplet digital PCR approaches to measure rDNA copy number in normal and cancer states in human and mouse genomes. We find that copy number and sequence can change in cancer genomes...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28630377/effects-of-cognitive-reserve-depend-on-executive-and-semantic-demands-of-the-task
#17
R Ryan Darby, Michael Brickhouse, David A Wolk, Bradford C Dickerson
BACKGROUND: Cognitive reserve (CR) is one factor that helps to maintain cognitive function in patients with Alzheimer's disease (AD). Whether the effects of CR depend on the semantic/executive components of the task remains unknown. METHODS: 470 patients (138 with AD, 332 with mild cognitive impairment (MCI)) were selected from the Alzheimer's Disease Neuroimaging Initiative database. Linear regression models were used to determine the effects of CR (years of education) on cognitive performance after controlling for demographic factors and regional cortical atrophy...
June 19, 2017: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/28629339/droplet-digital-pcr-for-detection-and-quantification-of-circulating-tumor-dna-in-plasma-of-head-and-neck-cancer-patients
#18
Joost H van Ginkel, Manon M H Huibers, Robert J J van Es, Remco de Bree, Stefan M Willems
BACKGROUND: During posttreatment surveillance of head and neck cancer patients, imaging is insufficiently accurate for the early detection of relapsing disease. Free circulating tumor DNA (ctDNA) may serve as a novel biomarker for monitoring tumor burden during posttreatment surveillance of these patients. In this exploratory study, we investigated whether low level ctDNA in plasma of head and neck cancer patients can be detected using Droplet Digital PCR (ddPCR). METHODS: TP53 mutations were determined in surgically resected primary tumor samples from six patients with high stage (II-IV), moderate to poorly differentiated head and neck squamous cell carcinoma (HNSCC)...
June 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28625643/sequential-liquid-biopsies-reveal-dynamic-alterations-of-egfr-driver-mutations-and-indicate-egfr-amplification-as-a-new-mechanism-of-resistance-to-osimertinib-in-nsclc
#19
Franciele H Knebel, Fabiana Bettoni, Andrea K Shimada, Manoel Cruz, João Victor Alessi, Marcelo V Negrão, Luiz Fernando L Reis, Artur Katz, Anamaria A Camargo
Osimertinib is an EGFR-T790M-specific TKI, which has demonstrated impressive response rates in NSCLC, after failure to first-line anti-EGFR TKIs. However, acquired resistance to osimertinib is also observed and the molecular mechanisms of resistance are not yet fully understood. Monitoring and managing NSCLC patients who progressed on osimertinib is, therefore, emerging as an important clinical challenge. Sequential liquid biopsies were used to monitor a patient with EGFR-exon19del positive NSCLC, who received erlotinib and progressed through the acquisition of the EGFR-T790M mutation...
June 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28593555/genetic-analysis-of-irf6-a-gene-involved-in-craniofacial-midline-formation-in-relation-to-pituitary-and-facial-morphology-of-patients-with-idiopathic-growth-hormone-deficiency
#20
Eline Starink, Anita C S Hokken-Koelega, Theo J Visser, Janneke Baan, Robin P Peeters, Laura C G de Graaff
INTRODUCTION: Growth hormone is secreted by the pituitary gland, which forms part of the craniofacial midline. IRF6 encodes a transcription factor involved in the development of the craniofacial midline and mutations in IRF6 are known to disturb craniofacial development. Craniofacial and pituitary development are closely related. After whole exome sequencing revealed a new mutation in IRF6 in a family with Idiopathic Growth Hormone Deficiency (IGHD), we screened the remainder of our IGHD cohort for mutations in this gene and related their genotypes to pituitary and craniofacial morphology...
June 7, 2017: Pituitary
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