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next generation sequencing analysis

Małgorzata Dawidowska, Roman Jaksik, Monika Drobna, Bronisława Szarzyńska-Zawadzka, Maria Kosmalska, Łukasz Sędek, Ludomiła Machowska, Anna Lalik, Monika Lejman, Marek Ussowicz, Krzysztof Kałwak, Jerzy R Kowalczyk, Tomasz Szczepański, Michał Witt
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy originating from T-cell precursors. The genetic landscape of T-ALL has been largely characterized by next-generation sequencing. Yet, the transcriptome of miRNAs (miRNome) of T-ALL has been less extensively studied. Using small RNA sequencing, we characterized the miRNome of 34 pediatric T-ALL samples, including the expression of isomiRs and the identification of candidate novel miRNAs (not previously annotated in miRBase). For the first time, we show that immunophenotypic subtypes of T-ALL present different miRNA expression profiles...
February 11, 2019: Neoplasia: An International Journal for Oncology Research
Juan Carlos Ruiz-Cabezas, Francisco Barros, Beatriz Sobrino, Gustavo García, Ramiro Burgos, Carlos Farhat, Antonella Castro, Lenin Muñoz, Ana Karina Zambrano, Mariela Martínez, Martha Montalván, César Paz-Y-Miño
The frequency distributions of cystic fibrosis variants are heterogeneous in Ecuador because of the genetic admixture of its population. The aim of this study was to identify disease-causing variants among Ecuadorian cystic fibrosis (CF) patients by next-generation sequencing (NGS) of the entire cystic fibrosis transmembrane conductance regulator (CFTR) gene. The results showed an approximation of the frequencies of pathogenic variants in the population under study and an optimal mutation panel for routine first-line CF molecular diagnosis...
February 11, 2019: Gene
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies...
February 14, 2019: PLoS Computational Biology
Xiaohui Wu, Xingqiang Gao, Peng Han, Yulin Zhou
BACKGROUND: Due to extreme genetic heterogeneity, targeted next-generation sequencing (NGS) can be an efficient tool for rapid genetic diagnosis of hereditary non-syndromic hearing loss (NSHL). AIMS/OBJECTIVES: This study was aiming to identify causative variants in NSHL patients from the Minnan region through targeted NGS. MATERIAL AND METHODS: Genomic DNA samples from 90 NSHL subjects were extracted and subjected to SureSelect target enrichment system to capture the entire coding exons and flanking intronic regions of gene GJB2, SLC26A4, and MT-RNR1...
February 14, 2019: Acta Oto-laryngologica
Meng-Jiao Zhu, Xiao-Yun Ma, Pei-Cheng Ding, Han-Fei Tang, Rui Peng, Lei Lu, Pei-Qiang Li, Bin Qiao, Xue-Yan Yang, Yu-Fang Zheng, Hong-Yan Wang, Yun-Qian Gao, Feng-Shan Chen
Congenital heart defects (CHDs), the most common congenital human birth anomalies, involves complex genetic factors. Wnt/β-catenin pathway is critical for cardiogenesis and proved to be associated with numerous congenital heart abnormities. AXIN2 has a unique role in Wnt/β-catenin pathway, as it is not only an important inhibitor but also a direct target of Wnt/β-catenin pathway. However, whether AXIN2 is associated with human CHDs has not been reported. In our present study, we found a differential expression of Axin2 mRNA during the development of mouse heart, indicating its importance in mouse cardiac development...
February 13, 2019: Journal of Human Genetics
Mansour Alsaleem, Michael S Toss, Chitra Joseph, Mohammed Aleskandarany, Sasagu Kurozumi, Ibrahim Alshankyty, Angela Ogden, Padmashree C G Rida, Ian O Ellis, Ritu Aneja, Andrew R Green, Nigel P Mongan, Emad A Rakha
E-cadherin is a tumor suppressor gene in invasive lobular breast cancer. However, a proportion of high-grade ductal carcinoma shows reduced/loss of E-cadherin. In this study, we assessed the underlying mechanisms and molecular implications of E-cadherin loss in invasive ductal carcinoma. This study used large, well-characterized cohorts of early-stage breast cancer-evaluated E-cadherin expression via various platforms including immunohistochemistry, microarray analysis using Illumina HT-12 v3, copy number analysis using Affymetrix SNP 6...
February 13, 2019: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Kazuki Suzuki, Manami Takemura, Takaaki Miki, Masanori Nonaka, Naoki Harada
Soil bacterial community compositions and temporal changes in organic paddy fields were elucidated using a 16S rRNA gene amplicon sequencing analysis with a high-throughput next generation sequencer. At transplanting, bacterial community compositions in organic and conventional paddy fields were mostly similar despite differences in field management. The bacterial community composition in organic fields differed from that under conventional management during the rice growth period, possibly as a result of the decomposition process of organic fertilizers...
February 13, 2019: Microbes and Environments
Nahyeon Kang, Su Yeon Choi, Bit Na Kim, Chang Dong Yeo, Chan Kwon Park, Young Kyoon Kim, Tae-Jung Kim, Seong-Beom Lee, Sug Hyung Lee, Jong Y Park, Mi Sun Park, Hyeon Woo Yim, Seung Joon Kim
BACKGROUND: A hypoxic microenvironment leads to an increase in the invasiveness and the metastatic potential of cancer cells within tumors via the epithelial-mesenchymal transition (EMT) and cancer stemness acquisition. However, hypoxia-induced changes in the expression and function of candidate stem cell markers and their possible molecular mechanism is still not understood. METHODS: Lung cell lines were analyzed in normoxic or hypoxic conditions. For screening among the stem cell markers, a transcriptome analysis using next-generation sequencing was performed...
February 13, 2019: BMC Cancer
Ryan Barrett, Cynthia L Neben, Anjali D Zimmer, Gilad Mishne, Wendy McKennon, Alicia Y Zhou, Jeremy Ginsberg
Next generation sequencing multi-gene panels have greatly improved the diagnostic yield and cost effectiveness of genetic testing and are rapidly being integrated into the clinic for hereditary cancer risk. With this technology comes a dramatic increase in the volume, type and complexity of data. This invaluable data though is too often buried or inaccessible to researchers, especially to those without strong analytical or programming skills. To effectively share comprehensive, integrated genotypic-phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Maha Farhat, Khaled R Alkharsah, Fatimah I Alkhamis, Huda A Bukharie
Bacterial community diversity of bulk water and corresponding biofilms of four intensive care units' (ICUs) drinking water systems were studied and compared using 16S rRNA gene amplicons and next generation sequencing. Proteobacteria, mainly Alphaproteobacteria and Betaproteobacteria were dominant in the bulk water and biofilms. Principal component analysis showed different bacterial communities characterizing each of the bulk water and the biofilms in three of the studied ICUs. Taxonomic classification and comparison of different genera between samples highlighted the dominance of Aquabacterium (80%) and Novosphingobium (72%) in bulk water while biofilms harbored different bacteria affiliated to Pelomonas (97%) and Caulobacter (96%), Porphyrobacter (78%) and Staphylococcus (74%)...
February 2019: Journal of Water and Health
Mona Mahfood, Walaa Kamal Eddine Ahmad Mohamed, Abdullah Al Mutery, Abdelaziz Tlili
AIMS: Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common form of hereditary deafness. Despite its frequency, the diagnosis of this disorder continues to be a challenging task given its extreme genetic heterogeneity. The purpose of this study was to identify the causative mutation in a consanguineous United Arab Emirates (UAE) family with ARNSHL. MATERIALS AND METHODS: Clinical exome sequencing (CES) followed by segregation analysis via Sanger sequencing was used to identify the causative mutation...
February 13, 2019: Genetic Testing and Molecular Biomarkers
Dayane de Melo Costa, Khalid Johani, Dulcelene Sousa Melo, Lillian Kelly de Oliveira Lopes, Liwcy Keller de Oliveira Lopes Lima, Anaclara Ferreira Veiga Tipple, Honghua Hu, Karen Vickery
The aim of this study was to determine the epidemiology (location, microbial load, microbiome, presence/absence of biofilm, and pathogens, including ESKAPE - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species, and antimicrobial susceptibility profiles) of the bacterial contamination on intensive care units (ICUs) surfaces. Fifty-seven high-touched surfaces were collected from adult, paediatric and neonatal ICUs from two large public Brazilian hospitals from central and north regions...
February 13, 2019: Letters in Applied Microbiology
Takashi Yoshida, Tatsuya Yamaguchi, Shinya Maekawa, Shinichi Takano, Toru Kuno, Keisuke Tanaka, Fumihiko Iwamoto, Yuya Tsukui, Shoji Kobayashi, Yukiko Asakawa, Hiroko Shindo, Mitsuharu Fukasawa, Yasuhiro Nakayama, Taisuke Inoue, Tomoyoshi Uetake, Masahiko Ohtaka, Tadashi Sato, Kunio Mochizuki, Nobuyuki Enomoto
BACKGROUND AND AIMS: The recent advancement of next-generation sequencing (NGS) has enabled the identification of cancer-related somatic aberrations in advanced gastric cancer. However, these remain unclear in early gastric cancers, especially in intramucosal gastric cancers. PATIENTS AND METHODS: Thirty-one well-differentiated (tub1) intramucosal gastric cancers obtained by endoscopic submucosal dissection (ESD) from 29 patients were analyzed. After precise collection of tumors and non-tumors from formalin-fixed paraffin-embedded tissues using laser-captured microdissection (LCM), target sequencing analysis of 50 cancer-related genes was performed using an Ion-Proton sequencer...
February 11, 2019: Gastric Cancer
Soo Ki Kim, Haruhiko Takeda, Atsushi Takai, Tomonori Matsumoto, Nobuyuki Kakiuchi, Akira Yokoyama, Kenichi Yoshida, Toshimi Kaido, Shinji Uemoto, Sachiko Minamiguchi, Hironori Haga, Yuichi Shiraishi, Satoru Miyano, Hiroshi Seno, Seishi Ogawa, Hiroyuki Marusawa
BACKGROUND: Hepatocellular carcinoma (HCC) recurrently develops in cirrhotic liver containing a number of regenerative nodules (RNs). However, the biological tumorigenic potential of RNs is still unclear. To uncover the molecular bases of tumorigenesis in liver cirrhosis, we investigated the genetic aberrations in RNs of cirrhotic tissues using next-generation sequencing. METHODS: We isolated 205 RNs and 7 HCC tissues from the whole explanted livers of 10 randomly selected patients who had undergone living-donor liver transplantation...
February 12, 2019: Journal of Gastroenterology
Zhen-Shan Deng, Bao-Cheng Zhang, Xiang-Ying Qi, Zhi-Hong Sun, Xiao-Long He, Yu-Zhen Liu, Jing Li, Kai-Kai Chen, Zhan-Xi Lin
Pennisetum sinese , a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of "Green for Grain" project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P...
February 11, 2019: Microorganisms
Sophia R Chaudhry, Michael A Tainsky
Molecular genetic testing provides the capability for personalized prediction, diagnosis, and pharmacological treatments of disease and disorders. Variant assessment of next-generation sequencing (NGS) is a crucial component of genetic testing for clinicians to counsel patients on risk and management. The iVariantGuide application is a dynamic Web-based application made for the tertiary analysis of NGS. Along with variant assessment, iVariantGuide provides a unique interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analysis...
February 12, 2019: Current Protocols in Bioinformatics
Tihana Ibrahimpasic, Ronald Ghossein, Jatin P Shah, Ian Ganly
BACKGROUND: Poorly differentiated thyroid cancer (PDTC) is a rare but clinically highly significant entity because it accounts for most fatalities from non-anaplastic follicular cell-derived thyroid cancer. Due to the relative rarity of the disease and heterogeneous diagnostic criteria, studies on PDTC have been limited. In light of the evolution of ultra deep next-generation sequencing (NGS) technologies and through correlation of clinico-pathological and genomic characteristics of PDTC, an improved understanding of the biology of PDTC has been facilitated...
February 12, 2019: Thyroid: Official Journal of the American Thyroid Association
Jian Wu, Wei Dai, Lin Wu, Weiwei Li, Xinyi Xia, Jinke Wang
Cell free DNA (cfDNA) in human plasma carries abundant information, which has therefore been the key sample for non-invasive prenatal testing (NIPT) and liquid biopsy. Especially by using the rapidly developed next-generation sequencing (NGS) techniques, the genetic and epigenetic information embedded in cfDNA has been effectively and extensively decoded. In this process, a key step is to construct the NGS library. Due to its high degradation, the single strand-based method was reported to be more qualified to construct the NGS library of cfDNA...
February 12, 2019: International Journal of Cancer. Journal International du Cancer
Pengpeng Zhang, Yingzi Ming, Ke Cheng, Ying Niu, Qifa Ye
Ischemic postconditioning (IPO) attenuates hepatic ischemia/reperfusion (I/R) injury. However, little is known about the underlying biological pathophysiology, which could be, at least in part, informed by exploring the transcriptomic changes using next-generation RNA sequencing (RNA-Seq). In this study, 18 mice (C57BL/6) were involved and randomly assigned to three groups: normal (n=6), I/R (n=6, subjected to 70% hepatic I/R), and IR+IPO (n=6, applying IPO to mice with I/R injury). We randomly selected 3 mice per group and extracted their liver tissues for next-generation RNA-Seq...
2019: International Journal of Medical Sciences
Zhicheng Huang, Zhiqiang Sun, Xueying Zhang, Kai Niu, Ying Wang, Jun Zheng, Hang Li, Ying Liu
PIEZO channels involve in wound sealing, cell  proliferation in many cell types. Recent study in lung cancer by using next generation sequencing analysis has indicated that PIEZOs' functions were implicated in LC development. However, the expression and role of PIEZO channels in non-small cell lung cancer (NSCLC) progression remain elusive. In current study, we investigated the gene expression and alteration frequency in human NSCLC tissue, accessed the prognostic roles of PIEZO channels in NSCLC patients, and further studied the effect of PIEZOs in NSCLC cells proliferation and tumor growth in vivo...
February 11, 2019: Bioscience Reports
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