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https://www.readbyqxmd.com/read/29667179/characteristics-of-genomic-alterations-of-lung-adenocarcinoma-in-young-never-smokers
#1
Wenxin Luo, Panwen Tian, Yue Wang, Heng Xu, Lu Chen, Chao Tang, Yang Shu, Shouyue Zhang, Zhoufeng Wang, Jun Zhang, Li Zhang, Lili Jiang, Lunxu Liu, Guowei Che, Chenglin Guo, Hong Zhang, Jiali Wang, Weimin Li
Non-small cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger...
April 18, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29666669/-egfr-amplification-induces-sensitivity-to-anti-egfr-therapy-in-pancreatic-acinar-cell-carcinoma
#2
Corentin Richard, Julie Niogret, Romain Boidot, Francois Ghiringhelli
Pancreatic acinar cell carcinoma (PACC) is a rare cancer. When the tumor is metastatic, few therapeutic options are available. Precision medicine using next-generation sequencing is defined by the administration of drugs based on the tumor genetic mutations. The usage of precision medicine for finding new therapeutic options for rare cancers is an emerging field. We have reported here the case of a patient bearing a multitreated metastatic PACC. This patient underwent somatic and constitutional exome analyses...
April 15, 2018: World Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/29666626/next-generation-immune-repertoire-sequencing-as-a-clue-to-elucidate-the-landscape-of-immune-modulation-by-host-gut-microbiome-interactions
#3
Tatsuo Ichinohe, Takahiko Miyama, Takakazu Kawase, Yasuko Honjo, Kazutaka Kitaura, Hiroyuki Sato, Tadasu Shin-I, Ryuji Suzuki
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29666446/life-on-the-edge-active-microbial-communities-in-the-kryos-mgcl-2-brine-basin-at-very-low-water-activity
#4
Lea Steinle, Katrin Knittel, Nicole Felber, Claudia Casalino, Gert de Lange, Chiara Tessarolo, Alina Stadnitskaia, Jaap S Sinninghe Damsté, Jakob Zopfi, Moritz F Lehmann, Tina Treude, Helge Niemann
The Kryos Basin is a deep-sea hypersaline anoxic basin (DHAB) located in the Eastern Mediterranean Sea (34.98°N 22.04°E). It is filled with brine of re-dissolved Messinian evaporites and is nearly saturated with MgCl2 -equivalents, which makes this habitat extremely challenging for life. The strong density difference between the anoxic brine and the overlying oxic Mediterranean seawater impedes mixing, giving rise to a narrow chemocline. Here, we investigate the microbial community structure and activities across the seawater-brine interface using a combined biogeochemical, next-generation sequencing, and lipid biomarker approach...
April 17, 2018: ISME Journal
https://www.readbyqxmd.com/read/29666441/using-biology-to-guide-the-treatment-of-sarcomas-and-aggressive-connective-tissue-tumours
#5
REVIEW
Armelle Dufresne, Mehdi Brahmi, Marie Karanian, Jean-Yves Blay
Sarcomas are a heterogeneous group of malignancies that arise from cells of a mesenchymal origin. Surgery forms the mainstay of the treatment of most patients with localized sarcoma and might be followed or preceded by chemotherapy and/or radiotherapy. In the metastatic setting, systemic treatments tend to improve survival and control symptoms. However, the adverse events and sometimes disappointing outcomes associated with these empirical approaches to treatment indicate a need for new approaches. The advent of next-generation sequencing (NGS) has enabled more targeted treatment of many malignancies based on the presence of specific alterations...
April 17, 2018: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/29666403/intact-interleukin-10-receptor-signaling-protects-from-hippocampal-damage-elicited-by-experimental-neurotropic-virus-infection-of-sjl-mice
#6
Ann-Kathrin Uhde, Malgorzata Ciurkiewicz, Vanessa Herder, Muhammad Akram Khan, Niko Hensel, Peter Claus, Michael Beckstette, René Teich, Stefan Floess, Wolfgang Baumgärtner, Klaus Jung, Jochen Huehn, Andreas Beineke
Theiler's murine encephalomyelitis virus (TMEV) infection represents an experimental mouse model to study hippocampal damage induced by neurotropic viruses. IL-10 is a pleiotropic cytokine with profound anti-inflammatory properties, which critically controls immune homeostasis. In order to analyze IL-10R signaling following virus-induced polioencephalitis, SJL mice were intracerebrally infected with TMEV. RNA-based next generation sequencing revealed an up-regulation of Il10, Il10rα and further genes involved in IL-10 downstream signaling, including Jak1, Socs3 and Stat3 in the brain upon infection...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666117/novel-insights-into-the-pathogenesis-of-t-cell-lymphomas
#7
John S Van Arnam, Megan S Lim, Kojo S J Elenitoba-Johnson
T-cell lymphomas are a heterogeneous group of rare malignancies with overlapping clinical, immunologic and histologic features. Recent advances in our understanding of T-cell differentiation based on gene expression profiling, next-generation sequencing (NGS) and transgenic mouse modeling studies have better elucidated the pathogenetic mechanisms underlying the diverse biology of T-cell lymphomas. These studies show that while genetic alterations in epigenetic modifiers are implicated in all subtypes of T-cell lymphomas, specific subtypes demonstrate enrichment for particular recurrent alterations targeting specific genes...
April 17, 2018: Blood
https://www.readbyqxmd.com/read/29665853/microsatellite-instability-in-prostate-cancer-by-pcr-or-next-generation-sequencing
#8
Jennifer A Hempelmann, Christina M Lockwood, Eric Q Konnick, Michael T Schweizer, Emmanuel S Antonarakis, Tamara L Lotan, Bruce Montgomery, Peter S Nelson, Nola Klemfuss, Stephen J Salipante, Colin C Pritchard
BACKGROUND: Microsatellite instability (MSI) is now being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer. Yet current molecular diagnostic tests for MSI have not been evaluated for use in prostate cancer. METHODS: We evaluated two next-generation sequencing (NGS) MSI-detection methods, MSIplus (18 markers) and MSI by Large Panel NGS (> 60 markers), and compared the performance of each NGS method to the most widely used 5-marker MSI-PCR detection system...
April 17, 2018: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/29665843/next-generation-sequencing-analysis-of-receptor-type-tyrosine-kinase-genes-in-surgically-resected-colon-cancer-identification-of-gain-of-function-mutations-in-the-ret-proto-oncogene
#9
Duarte Mendes Oliveira, Katia Grillone, Chiara Mignogna, Valentina De Falco, Carmelo Laudanna, Flavia Biamonte, Rosa Locane, Francesco Corcione, Massimiliano Fabozzi, Rosario Sacco, Giuseppe Viglietto, Donatella Malanga, Antonia Rizzuto
BACKGROUND: Improvement in genetic characterization of Colon Cancer (CC) patients is required to propose new potential targets, since surgical resection coupled to chemotherapy, presents several limits such as cancer recurrence and drug resistance. Targeted therapies have more efficacy and less toxicity than standard treatments. One of the most relevant cancer-specific actionable targets are receptor tyrosine kinases (RTKs) whose role in CC need to be better investigated. METHODS: We have analysed 37 CC patients using the Ion AmpliSeq™ Comprehensive Cancer Panel (CCP)...
April 17, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29665779/a-machine-learning-model-to-determine-the-accuracy-of-variant-calls-in-capture-based-next-generation-sequencing
#10
Jeroen van den Akker, Gilad Mishne, Anjali D Zimmer, Alicia Y Zhou
BACKGROUND: Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read depth, and mapping accuracy. With recent advances in NGS technology and software tools, the majority of variants called using NGS alone are in fact accurate and reliable. However, a small subset of difficult-to-call variants that still do require orthogonal confirmation exist...
April 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29664913/cost-benefit-analysis-of-introducing-next-generation-sequencing-metagenomic-pathogen-testing-in-the-setting-of-pyrexia-of-unknown-origin
#11
Jia Hui Chai, Chun Kiat Lee, Hong Kai Lee, Nicholas Wong, Kahwee Teo, Chuen Seng Tan, Praveen Thokala, Julian Wei-Tze Tang, Paul Anantharajah Tambyah, Vernon Min Sen Oh, Tze Ping Loh, Joanne Yoong
Pyrexia of unknown origin (PUO) is defined as a temperature of >38.3°C that lasts for >3 weeks, where no cause can be found despite appropriate investigation. Existing protocols for the work-up of PUO can be extensive and costly, motivating the application of recent advances in molecular diagnostics to pathogen testing. There have been many reports describing various analytical methods and performance of metagenomic pathogen testing in clinical samples but the economics of it has been less well studied...
2018: PloS One
https://www.readbyqxmd.com/read/29664687/distinctiveness-and-similarities-between-extended-spectrum-%C3%AE-lactamase-producing-escherichia-coli-isolated-from-cattle-and-the-community-in-israel
#12
Ziv Lifshitz, Na'ama Sturlesi, Miriam Parizade, Shlomo E Blum, Michal Gordon, Diana Taran, Amos Adler
The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), blaCTX-M gene allele, and mobile genetic elements (MGEs) surrounding it...
April 17, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29664468/unifying-cancer-and-normal-rna-sequencing-data-from-different-sources
#13
Qingguo Wang, Joshua Armenia, Chao Zhang, Alexander V Penson, Ed Reznik, Liguo Zhang, Thais Minet, Angelica Ochoa, Benjamin E Gross, Christine A Iacobuzio-Donahue, Doron Betel, Barry S Taylor, Jianjiong Gao, Nikolaus Schultz
Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing...
April 17, 2018: Scientific Data
https://www.readbyqxmd.com/read/29664366/equine-encephalosis-virus-in-india-2008
#14
Pragya D Yadav, César G Albariño, Dimpal A Nyayanit, Lisa Guerrero, M Harley Jenks, Prasad Sarkale, Stuart T Nichol, Devendra T Mourya
A virus isolated from a sick horse from India in 2008 was confirmed by next-generation sequencing analysis to be equine encephalosis virus (EEV). EEV in India is concerning because several species of Culicoides midge, which play a major role in EEV natural maintenance and transmission, are present in this country.
May 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29664320/16s-rrna-gene-primer-validation-for-bacterial-diversity-analysis-of-vegetable-products
#15
Miyo Nakano
High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria...
April 17, 2018: Journal of Food Protection
https://www.readbyqxmd.com/read/29663558/usefulness-of-bcor-gene-mutation-as-a-prognostic-factor-in-acute-myeloid-leukemia-with-intermediate-cytogenetic-prognosis
#16
Kazuki Terada, Hiroki Yamaguchi, Toshimitsu Ueki, Kensuke Usuki, Yutaka Kobayashi, Kenji Tajika, Seiji Gomi, Saiko Kurosawa, Riho Saito, Yutaka Furuta, Keiki Miyadera, Taichiro Tokura, Atushi Marumo, Ikuko Omori, Masahiro Sakaguchi, Yusuke Fujiwara, Shunsuke Yui, Takeshi Ryotokuji, Kunihito Arai, Tomoaki Kitano, Satoshi Wakita, Takahiro Fukuda, Koiti Inokuchi
BCOR gene is a transcription regulatory factor that plays an essential role in normal hematopoiesis. The wider introduction of next-generation sequencing technology has led to reports in recent years of mutations in the BCOR gene in acute myeloid leukemia (AML), but the related clinical characteristics and prognosis are not sufficiently understood. We investigated the clinical characteristics and prognosis of 377 de novo AML cases with BCOR or BCORL1 mutation. BCOR or BCORL1 gene mutations were found in 28 cases (7...
April 16, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29663171/prognostic-relevance-of-mutations-and-copy-number-alterations-assessed-with-targeted-next-generation-sequencing-in-idh-mutant-grade-ii-glioma
#17
Maarten M J Wijnenga, Pim J French, Hendrikus J Dubbink, Winand N M Dinjens, Peggy N Atmodimedjo, Johan M Kros, Ruth Fleischeuer, Clemens M F Dirven, Arnaud J P E Vincent, Martin J van den Bent
BACKGROUND: At current prognostication of low grade glioma remains suboptimal and might be improved with additional markers. These may guide treatment decisions, in particular on early adjuvant therapy versus wait and see after surgery. METHODS: We used a targeted Next-Generation Sequencing panel to assess mutational and copy number status of selected genes and chromosomes in a consecutive series of adult grade II supratentorial glioma, and assessed the impact of molecular markers of interest on overall survival...
April 16, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29662960/impact-of-oral-hygiene-discontinuation-on-supragingival-and-salivary-microbiomes
#18
D Belstrøm, M L Sembler-Møller, M A Grande, N Kirkby, S L Cotton, B J Paster, S Twetman, P Holmstrup
The purpose of the present study was to characterize and compare supragingival and salivary microbiotas during a 10-d period of oral hygiene discontinuation. We tested the hypothesis that the composition of the salivary microbiota will reflect local microbial changes associated with accumulated biofilm formation and maturation. Pooled supragingival plaque ( n = 145) and stimulated saliva ( n = 145) samples were collected and plaque and gingival indices were recorded from 29 orally healthy individuals at baseline, during oral hygiene discontinuation (days 4, 7, and 10), and 14 d after resumption of oral hygiene...
January 2018: JDR Clinical and Translational Research
https://www.readbyqxmd.com/read/29662631/overlap-at-the-molecular-and-immunohistochemical-levels-between-angioimmunoblastic-t-cell-lymphoma-and-a-subgroup-of-peripheral-t-cell-lymphomas-without-specific-morphological-features
#19
Rebeca Manso, Julia González-Rincón, Manuel Rodríguez-Justo, Giovanna Roncador, Sagrario Gómez, Margarita Sánchez-Beato, Miguel A Piris, Socorro M Rodríguez-Pinilla
The overlap of morphology and immunophenotype between angioimmunoblastic T-cell lymphoma (AITL) and other nodal peripheral T-cell lymphomas (n-PTCLs) is a matter of current interest whose clinical relevance and pathogenic background have not been fully established. We studied a series of 98 n-PTCL samples (comprising 57 AITL and 41 PTCL-NOS) with five TFH antibodies (CD10, BCL-6, PD-1, CXCL13, ICOS), looked for mutations in five of the genes most frequently mutated in AITL ( TET2 , DNMT3A, IDH2, RHOA and PLCG1 ) using the Next-Generation-Sequencing Ion Torrent platform, and measured the correlations of these characteristics with morphology and clinical features...
March 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29662487/acquisition-of-n-glycosylation-sites-in-immunoglobulin-heavy-chain-genes-during-local-expansion-in-parotid-salivary-glands-of-primary-sj%C3%A3-gren-patients
#20
Annie Visser, Marieke E Doorenspleet, Niek de Vries, Fred K L Spijkervet, Arjan Vissink, Richard J Bende, Hendrika Bootsma, Frans G M Kroese, Nicolaas A Bos
Previous studies revealed high incidence of acquired N-glycosylation sites acquired N-glycosylation sites in RNA transcripts encoding immunoglobulin heavy variable region (IGHV) 3 genes from parotid glands of primary Sjögren's syndrome (pSS) patients. In this study, next generation sequencing was used to study the extent of ac-Nglycs among clonally expanded cells from all IGVH families in the salivary glands of pSS patients. RNA was isolated from parotid gland biopsies of five pSS patients and five non-pSS sicca controls...
2018: Frontiers in Immunology
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