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clinical bioinformatics

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https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#1
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28537914/epigenomic-study-identifies-a-novel-mesenchyme-homeobox2-gli1-transcription-axis-involved-in-cancer-drug-resistance-overall-survival-and-therapy-prognosis-in-lung-cancer-patients
#2
Leonel Armas-López, Patricia Piña-Sánchez, Oscar Arrieta, Enrique Guzman de Alba, Blanca Ortiz-Quintero, Patricio Santillán-Doherty, David C Christiani, Joaquín Zúñiga, Federico Ávila-Moreno
Several homeobox-related gene (HOX) transcription factors such as mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug resistance, malignant progression and/or clinical prognostic responses in lung cancer patients; however, the mechanisms involved in these responses have yet to be elucidated. Here, an epigenomic strategy was implemented to identify novel MEOX2 gene promoter transcription targets and propose a new molecular mechanism underlying lung cancer drug resistance and poor clinical prognosis...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28535003/mirna%C3%A2-1271-inhibits-cell-proliferation-in-neuroglioma-by-targeting-fibronectin-1
#3
Jian Gong, Zhao-Xia Wang, Zhen-Ying Liu
miR-1271 is a multifunctional post-translational modulator, which is involved in several diseases. However, the association between microRNA (miR)‑1271 and fibronectin 1 (FN1) remains to be fully elucidated in neuroglioma. In the present study, it was hypothesized that a post‑translational mechanism of miR‑1271 regulates the expression of FN1 in the progression of neuroglioma. The present study aimed to investigate the clinical significance and underlying molecular mechanisms of miRNA‑1271 in the development of glioma...
May 19, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28534999/mir-370-regulates-cell-proliferation-and-migration-by-targeting-egfr-in-gastric-cancer
#4
Tao Ning, Haiyang Zhang, Xinyi Wang, Shuang Li, Le Zhang, Ting Deng, Likun Zhou, Rui Liu, Xia Wang, Ming Bai, Shaohua Ge, Hongli Li, Dingzhi Huang, Guoguang Ying, Yi Ba
Epidermal growth factor receptor (EGFR) is known to be overexpressed in ~30% of gastric cancer (GC) cases, and may serve as an effective biomarker for predicting the clinical benefit of anti-EGFR therapy. However, the mechanism underlying the regulation of EGFR expression remains unknown. Evidence indicates that post-transcriptional regulation may exist in the process of EGFR expression. In the present study, we aimed to explore whether miR-370 is involved in this process, and how it impacts the biological behaviors of GC cells...
May 23, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28534966/microrna-92a-promotes-epithelial-mesenchymal-transition-through-activation-of-pten-pi3k-akt-signaling-pathway-in-non-small-cell-lung-cancer-metastasis
#5
Chaojing Lu, Zhengxiang Shan, Jiang Hong, Lixin Yang
MicroRNAs (miRNAs) have important roles in various cancers, including non-small cell lung cancer (NSCLC). Although several miRNAs have reported to be involved in the development of NSCLC, understanding the regulatory roles of other miRNAs in NSCLC is essential. Therefore, the aim of the current study was to explore the roles and mechanisms of screened miRNAs in NSCLC. First, the differentially expressed miRNAs that were screened based on GSE29248 microarray data retrieved from Gene Expression Omnibus (GEO)...
May 16, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28534892/minimizing-next-generation-sequencing-errors-for-hiv-drug-resistance-testing
#6
José A Fernández-Caballero, Natalia Chueca, Eva Poveda, Federico García
Next-generation sequencing prototypes for the routine diagnosis of resistance to antiretrovirals approved for the treatment of HIV infection are now being used in many clinical diagnostic laboratories. As some of the next-generation sequencing platforms may be a source of errors, it is necessary to improve the currently available protocols and implement bioinformatic tools that may help to correctly identify the presence of resistance mutations with clinical impact. Several studies have addressed these issues in recent years...
May 23, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28533502/clinical-value-and-prospective-pathway-signaling-of-microrna-375-in-lung-adenocarcinoma-a-study-based-on-the-cancer-genome-atlas-tcga-gene-expression-omnibus-geo-and-bioinformatics-analysis
#7
Ting-Qing Gan, Wen-Jie Chen, Hui Qin, Su-Ning Huang, Li-Hua Yang, Ye-Ying Fang, Lin-Jiang Pan, Zu-Yun Li, Gang Chen
BACKGROUND Lung adenocarcinoma (LUAD) is the most frequent lung cancer. MicroRNAs (miRNAs) are believed to have fundamental roles in tumorigenesis of LUAD. Although miRNAs are broadly recognized in LUAD, the role of microRNA-375 in LUAD is still not fully elucidated. MATERIAL AND METHODS We evaluated the significance of miR-375 expression in LUAD by using analysis of a public dataset from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database and a literature review. Furthermore, we investigated the biological function of miR-375 by gene ontology enrichment and target prediction analysis...
May 23, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28532404/use-of-the-qiagen-genereader-ngs-system-for-detection-of-kras-mutations-validated-by-the-qiagen-therascreen-pcr-kit-and-alternative-ngs-platform
#8
Agus Darwanto, Anne-Mette Hein, Sascha Strauss, Yi Kong, Andrew Sheridan, Dan Richards, Eric Lader, Monika Ngowe, Timothy Pelletier, Danielle Adams, Austin Ricker, Nishit Patel, Andreas Kühne, Simon Hughes, Dan Shiffman, Dirk Zimmermann, Kai Te Kaat, Thomas Rothmann
BACKGROUND: The detection of somatic mutations in primary tumors is critical for the understanding of cancer evolution and targeting therapy. Multiple technologies have been developed to enable the detection of such mutations. Next generation sequencing (NGS) is a new platform that is gradually becoming the technology of choice for genotyping cancer samples, owing to its ability to simultaneously interrogate many genomic loci at massively high efficiency and increasingly lower cost. However, multiple barriers still exist for its broader adoption in clinical research practice, such as fragmented workflow and complex bioinformatics analysis and interpretation...
May 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28530238/micrornas-146a-b-5-and-425-3p-and-24-3p-are-markers-of-antidepressant-response-and-regulate-mapk-wnt-system-genes
#9
Juan Pablo Lopez, Laura M Fiori, Cristiana Cruceanu, Rixing Lin, Benoit Labonte, Hannah M Cates, Elizabeth A Heller, Vincent Vialou, Stacy M Ku, Christophe Gerald, Ming-Hu Han, Jane Foster, Benicio N Frey, Claudio N Soares, Daniel J Müller, Faranak Farzan, Francesco Leri, Glenda M MacQueen, Harriet Feilotter, Kathrin Tyryshkin, Kenneth R Evans, Peter Giacobbe, Pierre Blier, Raymond W Lam, Roumen Milev, Sagar V Parikh, Susan Rotzinger, Steven C Strother, Cathryn M Lewis, Katherine J Aitchison, Gayle M Wittenberg, Naguib Mechawar, Eric J Nestler, Rudolf Uher, Sidney H Kennedy, Gustavo Turecki
Antidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only ∼30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and 8 weeks after treatment. Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529696/in-silico-gene-expression-profiling-in-cannabis-sativa
#10
Luca Massimino
The cannabis plant and its active ingredients (i.e., cannabinoids and terpenoids) have been socially stigmatized for half a century. Luckily, with more than 430,000 published scientific papers and about 600 ongoing and completed clinical trials, nowadays cannabis is employed for the treatment of many different medical conditions. Nevertheless, even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills...
2017: F1000Research
https://www.readbyqxmd.com/read/28529006/validation-of-a-next-generation-sequencing-pipeline-for-the-molecular-diagnosis-of-multiple-inherited-cancer-predisposing-syndromes
#11
Paula Paulo, Pedro Pinto, Ana Peixoto, Catarina Santos, Carla Pinto, Patrícia Rocha, Isabel Veiga, Gabriela Soares, Catarina Machado, Fabiana Ramos, Manuel R Teixeira
Despite the growing knowledge of the genetic background behind the cancers that occur in a context of hereditary predisposition, personal or family cancer history may not be clear enough to support directional gene testing. Defined targeted next-generation sequencing gene panels allow identification of the causative disease mutations of multigene syndromes and differential diagnosis for syndromes with phenotypically overlapping characteristics. Herein, we established a next-generation sequencing analysis pipeline for the molecular diagnosis of multiple inherited cancer predisposing syndromes using the commercially available target sequencing panel TruSight Cancer...
May 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28528185/simvastatin-ameliorate-memory-deficits-and-inflammation-in-clinical-and-mouse-model-of-alzheimer-s-disease-via-modulating-the-expression-of-mir-106b
#12
Wenzhong Huang, Zhenyu Li, Liandong Zhao, Wei Zhao
BACKGROUND: Alzheimer's disease (AD) as a neurodegenerative brain disorder is a devastating pathology leading to disastrous cognitive impairments and dementia, and several studies have shown that AD is closely related to the inflammation, so anti-inflammatory treatment may provide therapeutic benefits. In this study, the effect of simvastatin on inflammation was investigated and the underlying mechanisms were explored. METHODS: First, we tested the effect of simvastatin on AD in clinical research...
May 18, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28526810/bioinformatics-and-in-vitro-experimental-analyses-identify-the-selective-therapeutic-potential-of-interferon-gamma-and-apigenin-against-cervical-squamous-cell-carcinoma-and-adenocarcinoma
#13
Pei-Ming Yang, Chia-Jung Chou, Ssu-Hsueh Tseng, Chien-Fu Hung
The clinical management and treatment of cervical cancer, one of the most commonly diagnosed cancers and a leading cause of cancer-related female death, remains a huge challenge for researchers and health professionals. Cervical cancer can be categorized into two major subtypes: common squamous cell carcinoma (SCC) and adenocarcinoma (AC). Although it is a relatively rare histological subtype of cervical cancer, there has been a steady increase in the incidences of AC. Therefore, new strategies to treat cervical cancer are urgently needed...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#14
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526043/management-of-rare-diseases-of-the-head-neck-and-teeth-results-of-a-french-population-based-prospective-8-year-study
#15
Lisa Friedlander, Rémy Choquet, Eva Galliani, Myriam de Chalendar, Claude Messiaen, Amélie Ruel, Marie-Paule Vazquez, Ariane Berdal, Corinne Alberti, Muriel De La Dure Molla
BACKGROUND: In the last ten years, national rare disease networks have been established in France, including national centres of expertise and regional ones, with storage of patient data in a bioinformatics tool. The aim was to contribute to the development and evaluation of health strategies to improve the management of patients with rare diseases. The objective of this study has been to provide the first national-level data concerning rare diseases of the head, neck and teeth and to assess the balance between demand and supply of care in France...
May 19, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28524153/transcriptome-analysis-of-mirna-lncrna-mrna-interactions-in-the-malignant-transformation-process-of-gastric-cancer-initiation
#16
Y Mao, R Liu, H Zhou, S Yin, Q Zhao, X Ding, H Wang
Gastric cancer is a common heterogeneous malignancy that is pathologically characterized by the development of chronic atrophic gastritis and dysplasia of the epithelium. The pathogenic mechanisms at the molecular level are completely unclear. In the present study, we first address the expression network and miRNA-lncRNA-mRNA interaction in the malignant transformation process from normal mucosa and atrophic gastritis to a tumor. First, the long non-coding RNA (lncRNA), micro RNA (miRNA) and messenger RNA (mRNA) expression profiles of normal gastric mucosa, atrophic gastritis, gastric cancer and the peri-tumor tissues were analyzed using microarrays...
May 19, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28522603/smad4-loss-is-associated-with-cetuximab-resistance-and-induction-of-mapk-jnk-activation-in-head-and-neck-cancer-cells
#17
Hiroyuki Ozawa, Ruchira Ranaweera, Evgeny Izumchenko, Eugene Makarev, Alex Zhavoronkov, Elana J Fertig, Jason D Howard, Ana Markovic, Atul Bedi, Rajani Ravi, Jimena Perez, Quynh-Thu Le, Christina S Kong, Richard C K Jordan, Hao Wang, Hyunseok Kang, Harry Quon, David Sidransky, Christine H Chung
Purpose: We previously demonstrated an association between decreased SMAD4 expression and cetuximab resistance in head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to further elucidate the clinical relevance of SMAD4 loss in HNSCC. Experimental Design: SMAD4 expression was assessed by immunohistochemistry in 130 newly diagnosed and 43 recurrent HNSCC patients. Correlative statistical analysis with clinicopathological data was also performed. OncoFinder, a bioinformatics tool, was used to analyze molecular signaling in TCGA tumors with low or high SMAD4 mRNA levels...
May 18, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#18
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520848/pattern-fusion-analysis-by-adaptive-alignment-of-multiple-heterogeneous-omics-data
#19
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen
Motivation: Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called "pattern fusion analysis" (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e...
May 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28520167/kmt2b-rare-missense-variants-in-generalized-dystonia
#20
Michael Zech, Robert Jech, Petra Havránková, Anna Fečíková, Riccardo Berutti, Dušan Urgošík, David Kemlink, Tim M Strom, Jan Roth, Evžen Růžička, Juliane Winkelmann
BACKGROUND: Recently a novel syndrome of childhood-onset generalized dystonia originating from mutations in lysine-specific methyltransferase 2B (KMT2B) has been reported. METHODS: We sequenced the exomes of 4 generalized dystonia-affected probands recruited from a Prague movement disorders center (Czech Republic). Bioinformatics analyses were conducted to select candidate causal variants in described dystonia-mutated genes. After cosegregation testing, checklists from the American College of Medical Genetics and Genomics were adopted to judge variant pathogenicity...
May 18, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
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