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https://www.readbyqxmd.com/read/28550812/molecular-characterization-of-human-adenoviruses-in-urban-wastewaters-using-next-generation-and-sanger-sequencing
#1
M Iaconelli, B Valdazo-González, M Equestre, A R Ciccaglione, C Marcantonio, S Della Libera, G La Rosa
Human adenoviruses (HAdVs) are of major public health importance and are associated with a variety of clinical manifestations, including gastroenteritis, respiratory, ocular and urinary tract infections. To study the occurrence, prevalence and diversity of HAdV species and types circulating in Italy, we conducted a large-scale molecular-epidemiological investigation, a yearlong monitoring of 22 wastewater treatment plants, covering 10 Italian regions, representative of northern, central, and southern Italy...
May 19, 2017: Water Research
https://www.readbyqxmd.com/read/28550387/correlation-of-c-met-expression-with-pd-l1-expression-in-metastatic-clear-cell-renal-cell-carcinoma-treated-by-sunitinib-first-line-therapy
#2
Solène-Florence Kammerer-Jacquet, Sarah Medane, Karim Bensalah, Jean-Christophe Bernhard, Mokrane Yacoub, Frantz Dupuis, Alain Ravaud, Grégory Verhoest, Romain Mathieu, Benoit Peyronnet, Angélique Brunot, Brigitte Laguerre, Alexandra Lespagnol, Jean Mosser, Frédéric Dugay, Marc-Antoine Belaud-Rotureau, Nathalie Rioux-Leclercq
BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is highly metastatic. Cabozantinib, an anti-angiogenic tyrosine kinase inhibitor that targets c-MET, provided interesting results in metastatic ccRCC treatment. OBJECTIVE: To understand better the role of c-MET in ccRCC, we assessed its status in a population of patients with metastatic ccRCC. PATIENTS AND METHODS: For this purpose, tumor samples were analyzed for c-MET expression by immunohistochemistry (IHC), for c-MET copy number alterations by fluorescence in situ hybridization (FISH), and for c-MET mutations by next generation sequencing (NGS) in a retrospective cohort of 90 primary ccRCC of patients with metastases treated by first-line sunitinib...
May 26, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/28549623/standardising-rna-profiling-based-biomarker-application-in-cancer-the-need-for-robust-control-of-technical-variables
#3
REVIEW
James P Stewart, Susan Richman, Tim Maughan, Mark Lawler, Philip D Dunne, Manuel Salto-Tellez
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation...
May 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#4
V Albrecht, C Zweiniger, V Surendranath, K Lang, G Schöfl, A Dahl, S Winkler, V Lange, I Böhme, A H Schmidt
The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences...
May 25, 2017: HLA
https://www.readbyqxmd.com/read/28547571/clinical-presentations-and-molecular-studies-of-invasive-renal-epithelioid-angiomyolipoma
#5
Cheng-Keng Chuang, Hsin Chia Angela Lin, Han-Yu Tasi, Kun-Han Lee, Yuting Kao, Fukai Leo Chuang, Ying-Hsu Chang, Po-Hung Lin, Chung-Yi Liu, See-Tong Pang
PURPOSE: Epithelioid angiomyolipoma (EAML) is a rare variant of renal angiomyolipoma with malignant potential, and the cytogenetic and clinical behavior of EAML remains a challenging issue. METHODS: We retrospectively analyze the clinical courses of five EAML, the use of everolimus on metastatic EAML, and next-generation sequencing (NGS) and polymerase chain reaction (PCR) studies to investigate the gene mutation of TSC and the impact of PI3K/Akt/mTOR signaling pathway in metastatic EAML...
May 25, 2017: International Urology and Nephrology
https://www.readbyqxmd.com/read/28547568/biofertilizers-and-sustainable-agriculture-exploring-arbuscular-mycorrhizal-fungi
#6
REVIEW
Nicholas O Igiehon, Olubukola O Babalola
Worldwide agricultural food production has to double in 2050 so as to feed the global increasing population while reducing dependency on conventional chemical fertilizers plus pesticides. To accomplish this objective, there is the need to explore the several mutualistic interactions between plant roots and rhizosphere microbiome. Biofertilization is the process of boosting the abundance of microorganisms such as arbuscular mycorrhizal fungi (AMF) in the natural plant rhizosphere which depicts a beneficial alternative to chemical fertilization practices...
May 25, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28546527/effect-of-necrosis-on-the-mirna-mrna-regulatory-network-in-crt-mg-human-astroglioma-cells
#7
So-Hee Ahn, Jung-Hyuck Ahn, Dong-Ryeol Ryu, Jisoo Lee, Min-Sun Cho, Youn-Hee Choi
Purpose: Glioblastoma multiforme (GBM) is the most common adult primary intracranial tumor. The remarkable features of GBM include central necrosis. MicroRNAs (miRNAs) have been considered as diagnostic/prognostic biomarkers for many cancers, including glioblastoma. However, the effect of necrosis on the miRNA expression profile and predicted miRNA-mRNA regulatory information remain unclear. The purpose of this study is to examine the effect of necrotic cells on the modulation of miRNA and mRNA expression profiles and miRNA-mRNA network in CRT-MG cells...
May 22, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28545961/pecc-correcting-contigs-based-on-paired-end-read-distribution
#8
Min Li, Binbin Wu, Xiaodong Yan, Junwei Luo, Yi Pan, Fang-Xiang Wu, Jianxin Wang
MOTIVATION: Cheap and fast next generation sequencing (NGS) technologies facilitate research of de novo assembly greatly. The reliability of contigs is critical to construct reliable scaffolding. However, contigs generated from most assemblers contain errors because of the limitation of assembly strategy and computation complexity. Among all these errors, the misassembly error is one of the most harmful types. RESULTS: In this paper, we propose a new method named "PECC" to identify and correct misassembly errors in contigs based on the paired-end read distribution...
May 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#9
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545050/prevalence-and-extent-of-heteroresistance-by-next-generation-sequencing-of-multidrug-resistant-tuberculosis
#10
Darwin J Operario, Alexander F Koeppel, Stephen D Turner, Yongde Bao, Suporn Pholwat, Sayera Banu, Suporn Foongladda, Stellah Mpagama, Jean Gratz, Oleg Ogarkov, Svetlana Zhadova, Scott K Heysell, Eric R Houpt
Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides. Across these gene regions, complete resistance or heteroresistance (defined as 1%-99% mutation) was present in at least one isolate in 6.3% of loci. The number of isolates with heteroresistance was highest for gyrA codon 94, rpoB codons 526 and 531, and embB codons 306, 372 and 406 (range 11-26% of isolates exhibited heteroresistance)...
2017: PloS One
https://www.readbyqxmd.com/read/28542514/panweb-a-web-interface-for-pan-genomic-analysis
#11
Yan Pantoja, Kenny Pinheiro, Allan Veras, Fabrício Araújo, Ailton Lopes de Sousa, Luis Carlos Guimarães, Artur Silva, Rommel T J Ramos
With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species...
2017: PloS One
https://www.readbyqxmd.com/read/28542463/insights-into-reston-virus-spillovers-and-adaption-from-virus-whole-genome-sequences
#12
César G Albariño, Lisa Wiggleton Guerrero, Harley M Jenks, Ayan K Chakrabarti, Thomas G Ksiazek, Pierre E Rollin, Stuart T Nichol
Reston virus (family Filoviridae) is unique among the viruses of the Ebolavirus genus in that it is considered non-pathogenic in humans, in contrast to the other members which are highly virulent. The virus has however, been associated with several outbreaks of highly lethal hemorrhagic fever in non-human primates (NHPs), specifically cynomolgus monkeys (Macaca fascicularis) originating in the Philippines. In addition, Reston virus has been isolated from domestic pigs in the Philippines. To better understand virus spillover events and potential adaption to new hosts, the whole genome sequences of representative Reston virus isolates were obtained using a next generation sequencing (NGS) approach and comparative genomic analysis and virus fitness analyses were performed...
2017: PloS One
https://www.readbyqxmd.com/read/28542346/novel-mutations-in-col4a3-col4a4-and-col4a5-in-chinese-patients-with-alport-syndrome
#13
Jian-Hong Liu, Xiu-Xiu Wei, Ang Li, Ying-Xia Cui, Xin-Yi Xia, Wei-Song Qin, Ming-Chao Zhang, Er-Zhi Gao, Jun Sun, Chun-Lin Gao, Feng-Xia Liu, Qiu-Yue Wu, Wei-Wei Li, Asan, Zhi-Hong Liu, Xiao-Jun Li
Alport syndrome (AS) is a clinically and genetically heterogeneous, progressive nephropathy caused by mutations in COL4A3, COL4A4, and COL4A5, which encode type IV collagen. The large sizes of these genes and the absence of mutation hot spots have complicated mutational analysis by routine polymerase chain reaction (PCR)-based approaches. Here, in order to design a rapid and effective method for the genetic diagnosis of AS, we developed a strategy by utilizing targeted capture associated with next-generation sequencing (NGS) to analyze COL4A3, COL4A4, and COL4A5 simultaneously in 20 AS patients...
2017: PloS One
https://www.readbyqxmd.com/read/28541638/role-and-clinical-application-of-next-generation-sequencing-ngs-for-ovarian-cancer
#14
EDITORIAL
Myong Cheol Lim, Leslie M Randall
No abstract text is available yet for this article.
July 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/28541490/glanet-genomic-loci-annotation-and-enrichment-tool
#15
Burçak Otlu, Can Firtina, Sündüz Keles, Oznur Tastan
Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. Results: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28540684/next-generation-sequencing-for-microrna-expression-profile
#16
Yue Hu, Wenjun Lan, Daniel Miller
Sequencing technologies have made considerable advancements. From the Sanger sequencing method to the next-generation sequencing (NGS) methods, and from the NGS methods to the third-generation sequencing methods, we can see the development thread of the sequencing technology. Currently, NGS is the main contender in the sequencing market. NGS technologies provide an opportunity to research the microRNA (miRNA) expression profiles in detail. The NGS platforms have their own special characteristics, but share some main ideas...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540358/dataset-of-the-transcribed-45s-ribosomal-rna-sequence-of-the-tree-crop-yerba-mate
#17
Patricia M Aguilera, Humberto J Debat, Mauro Grabiele
This contribution contains data related to the research article entitled "The 18S-25S ribosomal RNA unit of yerba mate (Ilex paraguariensis A. St.-Hil.)" (Aguilera et al., 2016) [1]. Through a bioinformatic approach involving NGS data, we provide information of the transcribed 45S ribosomal RNA (rRNA) sequence of yerba mate, the first reference for the Ilex L. genus. This dataset (Supplementary file 1) comprises information regarding the assembly and annotation of this rRNA unit. The generated data is applicable for comparative analysis and evolutionary studies among Ilex and related taxa...
June 2017: Data in Brief
https://www.readbyqxmd.com/read/28540249/liquid-biopsies-for-bladder-cancer
#18
EDITORIAL
Douglas G Ward, Richard T Bryan
The development of accurate urinary biomarkers for the non-invasive detection of urothelial bladder cancer (UBC) could transform patient pathways by reducing reliance on cystoscopy, and the identification of highly prognostic (or even predictive) biomarkers could better guide patient management. A number of approaches are being utilised to address these challenges in both urinary- and plasma-borne tumour DNA (tDNA), so-called "liquid biopsies". Next generation sequencing (NGS) and droplet digital PCR (ddPCR) allow detection of very low levels of such tDNA amongst a large excess of non-tumour DNA, the former permitting large mutation panels to be assessed and the latter potentially identifying ultrarare mutant alleles yet restricted for multiplexing...
April 2017: Translational Andrology and Urology
https://www.readbyqxmd.com/read/28540003/vsx1-and-sod1-mutation-screening-in-patients-with-keratoconus-in-the-south-of-iran
#19
Mahmood Nejabat, Payam Naghash, Hassan Dastsooz, Sanaz Mohammadi, Mohsen Alipour, Majid Fardaei
PURPOSE: To investigate mutations of visual system homeobox 1 (VSX1) and superoxide dismutase 1 (SOD1) in 20 patients with keratoconus in the south of Iran. METHODS: Twenty patients with keratoconus who had a positive familial history were enrolled in this study and gave informed consent for DNA analysis. Genomic DNA was extracted from peripheral blood lymphocytes. Polymerase chain reaction (PCR) was carried out to amplify exon 2 of SOD1 and its exon-intron boundary for the detection of a seven-base deletion in intron 2 of SOD1, and also all five exons of VSX1 and their exon-intron boundaries...
April 2017: Journal of Ophthalmic & Vision Research
https://www.readbyqxmd.com/read/28539923/analysis-on-fungal-diversity-in-rhizosphere-soil-of-continuous-cropping-potato-subjected-to-different-furrow-ridge-mulching-managements
#20
Shuhao Qin, Stephen Yeboah, Xuexue Xu, Yuhui Liu, Bin Yu
Knowledge about fungi diversity following different planting patterns could improve our understanding of soil processes and thus help us to develop sustainable management strategies. The objective of this study was to determine the impact of different furrow-ridge mulching techniques on fungal diversity in rhizosphere soil under continuous cropping system. The investigated treatments were: flat plot without mulch (CK); flat plot with mulch (T1); on-ridge planting with full mulch (T2); on-furrow planting with full mulch (T3); on-ridge planting with half mulch (T4); and on-furrow planting with half mulch (T5)...
2017: Frontiers in Microbiology
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