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https://www.readbyqxmd.com/read/29352043/prognostic-implications-of-multiplex-detection-of-kras-mutations-in-cell-free-dna-from-patients-with-pancreatic-ductal-adenocarcinoma
#1
Min Kyeong Kim, Sang Myung Woo, Boram Park, Kyong-Ah Yoon, Yun-Hee Kim, Jungnam Joo, Woo Jin Lee, Sung-Sik Han, Sang-Jae Park, Sun-Young Kong
BACKGROUND: Cell-free DNA (cfDNA) is known to provide potential biomarkers for predicting clinical outcome, but its value in pancreatic ductal adenocarcinoma (PDAC) has not been fully evaluated. The aim of this study was to evaluate the clinical applicability of quantitative analysis of multiplex KRAS mutations in cell-free DNA from patients with PDAC. METHODS: A total of 106 patients with PDAC were enrolled in this prospective study. The concentration and fraction of KRAS mutations were determined through multiplex detection of KRAS mutations in plasma samples by use of a droplet digital PCR kit (Bio-Rad)...
January 19, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29350029/a-microwell-array-method-for-rapid-generation-of-uniform-agarose-droplets-and-beads-for-single-molecule-analysis
#2
Xingrui Li, Dongfeng Zhang, Huimin Zhang, Zhichao Guan, Yanling Song, Ruochen Liu, Zhi Zhu, Chaoyong James Yang
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with pre-selectable diameters ranging from 20 µm to 100 µm can be produced with relative standard deviations less than 3...
January 19, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29348862/digital-gene-expression-analysis-in-mice-lung-with-coinfection-of-influenza-and-streptococcus-pneumoniae
#3
Jun Luo, Linlin Zhou, Hongren Wang, Zhen Qin, Li Xiang, Jie Zhu, Xiaojun Huang, Yuan Yang, Wanyi Li, Baoning Wang, Mingyuan Li
Influenza A virus (IAV) and Streptococcus pneumoniae (SP) are two major upper respiratory tract pathogens that can also cause infection in polarized bronchial epithelial cells to exacerbate disease in coinfected individuals which may result in significant morbidity. However, the underlying molecular mechanism is poorly understood. Here, we employed BALB/c ByJ mice inflected with SP, IAV, IAV followed by SP (IAV+SP) and PBS (Control) as models to survey the global gene expression using digital gene expression (DGE) profiling...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29345349/enhanced-phosphorylation-of-sphingosine-and-ceramide-sustains-the-exuberant-proliferation-of-endothelial-progenitors-in-kaposi-sarcoma
#4
Loubna Abdel Hadi, Francesca Calcaterra, Lucia Brambilla, Claudia Carenza, Giovanni Marfia, Silvia Della Bella, Laura Riboni
Endothelial colony-forming cells (ECFCs), a unique endothelial stem cell population, are highly increased in the blood of Kaposi sarcoma (KS) patients. KS-derived ECFCs (KS-ECFCs) are also endowed with increased proliferative and vasculogenic potential, thus suggesting that they may be precursors of KS spindle cells. However, the mechanisms underlying the increased proliferative activity of KS-ECFCs remain poorly understood. Sphingosine-1-phosphate (S1P) and ceramide-1-phosphate (C1P) are metabolically interconnected sphingoid mediators crucial to cell proliferation...
December 15, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29341374/validation-of-the-digital-pcr-system-in-tyrosine-kinase-inhibitor-resistant-egfr-mutant-non-small-cell-lung-cancer
#5
Katsuhiro Masago, Shiro Fujita, Akito Hata, Chiyuki Okuda, Yuko Yoshizumi, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata, Yasushi Yatabe
The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib...
January 17, 2018: Pathology International
https://www.readbyqxmd.com/read/29340107/a-comparison-of-arms-plus-and-droplet-digital-pcr-for-detecting-egfr-activating-mutations-in-plasma
#6
Xinxin Zhang, Ning Chang, Guohua Yang, Yong Zhang, Mingxiang Ye, Jing Cao, Jie Xiong, Zhiping Han, Shuo Wu, Lei Shang, Jian Zhang
In this study, we introduce a novel amplification refractory mutation system (ARMS)-based assay, namely ARMS-Plus, for the detection of epidermal growth factor receptor (EGFR) mutations in plasma samples. We evaluated the performance of ARMS-Plus in comparison with droplet digital PCR (ddPCR) and assessed the significance of plasma EGFR mutations in predicting efficacy of EGFR-tyrosine kinase inhibitor (TKI) regimen. A total of 122 advanced non-small cell lung cancer (NSCLC) patients were enrolled in this study...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339441/allele-specific-droplet-digital-pcr-combined-with-a-next-generation-sequencing-based-algorithm-for-diagnostic-copy-number-analysis-in-genes-with-high-homology-proof-of-concept-using-stereocilin
#7
Sami S Amr, Elissa Murphy, Elizabeth Duffy, Rojeen Niazi, Jorune Balciuniene, Minjie Luo, Heidi L Rehm, Ahmad N Abou Tayoun
BACKGROUND: Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS: We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing...
January 16, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29334548/plasma-and-intracellular-pharmacokinetics-of-tenofovir-in-patients-switched-from-tenofovir-disoproxil-fumarate-to-tenofovir-alafenamide
#8
Anthony T Podany, Sara H Bares, Joshua Havens, Ravi Dyavar Shetty, Jennifer O'neill, Sarah Lee, Courtney V Fletcher, Susan Swindells, Kimberly K Scarsi
OBJECTIVES: The aim of the study was to compare the intra-individual plasma and intracellular peripheral blood mononuclear cell (PBMC) pharmacokinetics (PK) of tenofovir (TFV) and its intracellular metabolite, tenofovir-diphosphate (TFV-DP) in patients switched from a fixed dose combination (FDC) tablet of tenofovir disoproxil fumarate (TDF)/ emtricitabine (FTC)/ elvitegravir (EVG)/ cobicistat (COBI) to a FDC containing tenofovir alafenamide (TAF)/FTC/EVG/COBI. DESIGN: A single arm, prospective, non-randomized, cross-over, PK study in patients receiving a TDF-containing regimen (TDF 300 mg/ FTC 200 mg/ EVG 150 mg/ COBI 150 mg) switched to a TAF-containing FDC regimen (TAF 10 mg/ FTC 200 mg/ EVG 150 mg/ COBI 150 mg)...
January 13, 2018: AIDS
https://www.readbyqxmd.com/read/29333205/high-aspect-ratio-induced-spontaneous-generation-of-monodisperse-picolitre-droplets-for-digital-pcr
#9
Xiaonan Xu, Haojun Yuan, Ruyuan Song, Miao Yu, Ho Yin Chung, Youmin Hou, Yuhe Shang, Hongbo Zhou, Shuhuai Yao
Droplet microfluidics, which involves micrometer-sized emulsion droplets on a microfabricated platform, has been demonstrated as a unique system for many biological and chemical applications. Robust and scalable generation of monodisperse droplets at high throughput is of fundamental importance for droplet microfluidics. Classic designs for droplet generation employ shear fluid dynamics to induce the breakup of droplets in a two-phase flow and the droplet size is sensitive to flow rate fluctuations, often resulting in polydispersity...
January 2018: Biomicrofluidics
https://www.readbyqxmd.com/read/29327201/allele-specific-biased-expression-of-the-cntn6-gene-in-ips-cell-derived-neurons-from-a-patient-with-intellectual-disability-and-3p26-3-microduplication-involving-the-cntn6-gene
#10
Maria M Gridina, Natalia M Matveeva, Veniamin S Fishman, Aleksei G Menzorov, Helen A Kizilova, Nikolay A Beregovoy, Igor I Kovrigin, Inna E Pristyazhnyuk, Igor P Oscorbin, Maxim L Filipenko, Anna A Kashevarova, Nikolay A Skryabin, Tatyana V Nikitina, Elena A Sazhenova, Ludmila P Nazarenko, Igor N Lebedev, Oleg L Serov
Copy number variations (CNVs) of the human CNTN6 gene caused by megabase-scale microdeletions or microduplications in the 3p26.3 region are often the cause of neurodevelopmental disorders, including intellectual disability and developmental delay. Surprisingly, patients with different copy numbers of this gene display notable overlapping of neuropsychiatric symptoms. The complexity of the study of human neuropathologies is associated with the inaccessibility of brain material. This problem can be overcome through the use of reprogramming technologies that permit the generation of induced pluripotent stem (iPS) cells from fibroblasts and their subsequent in vitro differentiation into neurons...
January 11, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29326285/prevalence-of-aflatoxin-associated-tp53r249s-mutation-in-hepatocellular-carcinoma-in-hispanics-in-south-texas
#11
Jingjing Jiao, Weibo Niu, Ying Wang, Keith Baggerly, Yuanqing Ye, Xifeng Wu, Dewitt Davenport, Jose Luis Almeda, Monica M Betancourt-Garcia, R Armour Forse, Heather L Stevenson, Gordon P Watt, Joseph B McCormick, Susan P Fisher-Hoch, Laura Beretta
We aimed to determine whether aflatoxin dietary exposure plays a role in the high incidence of hepatocellular carcinoma (HCC) observed among Hispanics in South Texas. We measured TP53R249S somatic mutation, hallmark of aflatoxin etiology in HCC, using droplet digital PCR and RFLP. TP53R249S mutation was detected in 3 of 41 HCC tumors from Hispanics in South Texas (7.3%). We also measured TP53R249S mutation in plasma cell-free DNA (cfDNA) from 218 HCC patients and 96 Hispanic subjects with advanced fibrosis or cirrhosis, from South Texas...
January 11, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#12
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29323170/droplet-digital-pcr-based-egfr-mutation-detection-with-an-internal-quality-control-index-to-determine-the-quality-of-dna
#13
Sung-Su Kim, Hyun-Jeung Choi, Jin Ju Kim, M Sun Kim, In-Seon Lee, Bohyun Byun, Lina Jia, Myung Ryurl Oh, Youngho Moon, Sarah Park, Joon-Seok Choi, Seoung Wan Chae, Byung-Ho Nam, Jin-Soo Kim, Jihun Kim, Byung Soh Min, Jae Seok Lee, Jae-Kyung Won, Soo Youn Cho, Yoon-La Choi, Young Kee Shin
In clinical translational research and molecular in vitro diagnostics, a major challenge in the detection of genetic mutations is overcoming artefactual results caused by the low-quality of formalin-fixed paraffin-embedded tissue (FFPET)-derived DNA (FFPET-DNA). Here, we propose the use of an 'internal quality control (iQC) index' as a criterion for judging the minimum quality of DNA for PCR-based analyses. In a pre-clinical study comparing the results from droplet digital PCR-based EGFR mutation test (ddEGFR test) and qPCR-based EGFR mutation test (cobas EGFR test), iQC index ≥ 0...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321551/aster-leafhopper-survival-and-reproduction-and-aster-yellows-transmission-under-static-and-fluctuating-temperatures-using-ddpcr-for-phytoplasma-quantification
#14
Md H Bahar, Tyler J Wist, Diana R Bekkaoui, Dwayne D Hegedus, Chrystel Y Olivier
Aster yellows (AY) is an important disease of Brassica crops and is caused by Candidatus Phytoplasma asteris and transmitted by the insect vector, Aster leafhopper (Macrosteles quadrilineatus). Phytoplasma-infected Aster leafhoppers were incubated at various constant and fluctuating temperatures ranging from 0 to 35 °C with the reproductive host plant barley (Hordium vulgare). At 0 °C, leafhopper adults survived for 18 days, but failed to reproduce, whereas at 35 °C insects died within 18 days, but successfully reproduced before dying...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29318988/morphometric-and-molecular-study-of-fasciola-isolates-from-ruminants-in-iran
#15
Elham Akhlaghi, Mohammad Ali Mohammadi, Naser Ziaali, Mohammad Reza Baneshi, Saeid Nasibi, Hossein Kamyabi, Sima Rostami, Majid Fasihi Harandi
OBJECTIVE: The purpose of the present study was morphometric and molecular characterization of Fasciola isolates from ruminants in Iran. METHODS: Flukes were collected from the livers of 54 naturally infected sheep and cattle. The proportion of body length to width (L/W) of each fresh fluke was measured using a digital caliper. We employed receiver operating characteristic (ROC) curve analysis to explore the reliability of L/W for differentiating the two species...
December 2017: Türkiye Parazitolojii Dergisi
https://www.readbyqxmd.com/read/29312652/tyrosine-kinase-inhibitor-sensitive-pdgfr%C3%AE-mutations-in-gist-two-cases-and-review-of-the-literature
#16
Pieter A Boonstra, Jourik A Gietema, Albert J H Suurmeijer, Matthew R Groves, Fernando de Assis Batista, Ed Schuuring, Anna K L Reyners
Gastrointestinal stromal tumors (GISTs) are rare mesenchymal malignancies of the gastrointestinal tract. Most GISTs harbor a c-KIT (80%) or a PDGFRα (10%) mutation that leads to constitutive activation of the tyrosine kinase receptor. Response to treatment with tyrosine kinase inhibitors (TKIs) is dependent on mutational status of the tumor. The most common mutation in PDGFRα, D842V, is known to be imatinib resistant. Almost all other PDGFRα mutations are imatinib sensitive. We describe two patients with a PDGFRα exon 18 mutated GIST responding to treatment with TKIs...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29305255/comparative-analysis-of-gene-expression-in-maternal-peripheral-blood-and-monocytes-during-spontaneous-preterm-labor
#17
Alison G Paquette, Oksana Shynlova, Mark Kibschull, Nathan D Price, Stephen J Lye
BACKGROUND: Preterm birth is the leading cause of newborn death worldwide, and is associated with significant cognitive and physiological challenges in later life. There is a pressing need to define the mechanisms that initiate spontaneous preterm labor , and for development of novel clinical biomarkers to identify high-risk pregnancies. Most preterm birth studies utilize fetal tissues, and there is limited understanding of the transcriptional changes that occur in mothers undergoing spontaneous preterm labor...
January 2, 2018: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29305225/droplet-digital-pcr-for-mutation-detection-in-formalin-fixed-paraffin-embedded-melanoma-tissues-a-comparison-with-sanger-sequencing-and-pyrosequencing
#18
Ashleigh C McEvoy, Benjamin A Wood, Nima M Ardakani, Michelle Pereira, Robert Pearce, Lester Cowell, Cleo Robinson, Fabienne Grieu-Iacopetta, Alexander J Spicer, Benhur Amanuel, Melanie Ziman, Elin S Gray
Identification of somatic mutations is crucial to guide therapeutic decisions for personalized melanoma treatment. However, genetic analysis of the tumor is usually performed on limited and often low-quality DNA, from tumors with low tumor cellularity and high tumor heterogeneity. Different mutation detection platforms exist with varying analytical sensitivities. Here we evaluated the detection of common mutations in BRAF, NRAS, and TERT-promoter in 40 melanoma formalin-fixed, paraffin-embedded tissues using droplet digital PCR (ddPCR), and compared the results to the detection rate obtained by Sanger sequencing and pyrosequencing...
January 2, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29305193/ultra-sensitive-droplet-digital-pcr-for-the-assessment-of-microchimerism-in-cellular-therapies
#19
David Kliman, Gloria Castellano-Gonzalez, Barbara Withers, Janine Street, Elizabeth Tegg, Oksana Mirochnik, Joey Lai, Leighton Clancy, David Gottlieb, Emily Blyth
Current techniques to assess chimerism after hematopoietic stem cell transplantation (HSCT) are limited in both sensitivity and precision. These drawbacks are problematic in the context of cellular therapies which frequently result in microchimerism (donor chimerism <1%). We have developed a highly sensitive droplet digital PCR (ddPCR) assay using commercially available regents with good performance throughout the range of clinically relevant chimerism measurements, including microchimerism. We tested the assay using spiked samples of known donor:recipient ratios and in clinical samples from HSCT recipients and patients enrolled on clinical trials of microtransplantation and 3rd party virus specific T cells (VST)...
January 2, 2018: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/29304224/in-vitro-differentiation-of-human-oocyte-like-cells-from-oogonial-stem-cells-single-cell-isolation-and-molecular-characterization
#20
Erica Silvestris, Paola Cafforio, Stella D'Oronzo, Claudia Felici, Franco Silvestris, Giuseppe Loverro
STUDY QUESTION: Are the large cells derived from cultured DEAD box polypeptide 4 (DDX4)-positive oogonial stem cells (OSCs), isolated from the ovarian cortex of non-menopausal and menopausal women, oocyte-like cells? SUMMARY ANSWER: Under appropriate culture conditions, DDX4-positive OSCs from non-menopausal and menopausal women differentiate into large haploid oocyte-like cells expressing the major oocyte markers growth differentiation factor 9 (GDF-9) and synaptonemal complex protein 3 (SYCP3) and then enter meiosis...
January 3, 2018: Human Reproduction
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