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next generation sequencing analysis

Lingfang Feng, Jianlin Lou
DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Profiling DNA methylation across the genome is critical to understanding the influence of methylation in normal biology and diseases including cancer...
2019: Methods in Molecular Biology
Nobuyuki Bandoh, Toshiaki Akahane, Takashi Goto, Michihisa Kono, Haruyuki Ichikawa, Takahiro Sawada, Tomomi Yamaguchi, Hiroshi Nakano, Yumiko Kawase, Yasutaka Kato, Hajime Kamada, Yasuaki Harabuchi, Kazuo Shimizu, Hiroshi Nishihara
Thyroid carcinoma (TC) has characteristic genetic alterations, including point mutations in proto-oncogenes and chromosomal rearrangements that vary by histologic subtype. Recent developments in next-generation sequencing (NGS) technology enable simultaneous analysis of cancer-associated genes of interest, thus improving diagnostic accuracy and allowing precise personalized treatment for human cancer. A total of 50 patients who underwent thyroidectomy between 2014 and 2016 at Hokuto Hospital were enrolled. Total DNA was extracted from formalin-fixed, paraffin-embedded tissue sections and quantified...
December 2018: Oncology Letters
Jonathan Harris-Ricardo, Luis Fang, Alejandra Herrera-Herrera, Natalia Fortich-Mesa, Doris Olier-Castillo, Diana Cavanzo-Rojas, Roberto González-Quintero
OBJECTIVE: Tdescribe the bacterial profile of the supragingival biofilm of children with temporary dentition (CTD) and early mixed dentition (CEMD), with the next-generation sequencing (HOMINGS) technique. METHOD: A comparative descriptive study was carried out with 30 systemically healthy children aged between 5 and 7 years old from public schools in Cartagena-Colombia. All participants were caries-free applying the criteria of the International Caries Detection and Assessment System (ICDAS II) and had no caries experience according to the Decayed, Missing and Filled Teeth (DMFT) index...
December 10, 2018: Enfermedades Infecciosas y Microbiología Clínica
Yi-Jen Chen, Wei-An Chang, Ling-Yu Wu, Ya-Ling Hsu, Chia-Hsin Chen, Po-Lin Kuo
The phenotypic change of chondrocytes and the interplay between cartilage and subchondral bone in osteoarthritis (OA) has received much attention. Structural changes with nerve ingrowth and vascular penetration within OA cartilage may contribute to arthritic joint pain. The aim of this study was to identify differentially expressed genes and potential miRNA regulations in OA knee chondrocytes through next-generation sequencing and bioinformatics analysis. Results suggested the involvement of SMAD family member 3 ( SMAD3 ) and Wnt family member 5A ( WNT5A ) in the growth of blood vessels and cell aggregation, representing features of cartilage damage in OA...
December 10, 2018: Journal of Clinical Medicine
Pilar Garcia-Jimenez, Carlos Llorens, Francisco J Roig, Rafael R Robaina
Grateloupia imbricata is an intertidal marine seaweed and candidate model organism for both industry and academic research, owing to its ability to produce raw materials such as carrageenan. Here we report on the transcriptome of G. imbricata with the aim of providing new insights into the metabolic pathways and other functional pathways related to the reproduction of Grateloupia species. Next-generation sequencing was carried out with subsequent de novo assembly and annotation using state-of-the-art bioinformatic protocols...
December 7, 2018: Marine Drugs
Karolina Skonieczna-Żydecka, Wojciech Marlicz, Agata Misera, Anastasios Koulaouzidis, Igor Łoniewski
The central nervous system (CNS) and the human gastrointestinal (GI) tract communicate through the gut-brain axis (GBA). Such communication is bi-directional and involves neuronal, endocrine, and immunological mechanisms. There is mounting data that gut microbiota is the source of a number of neuroactive and immunocompetent substances, which shape the structure and function of brain regions involved in the control of emotions, cognition, and physical activity. Most GI diseases are associated with altered transmission within the GBA that are influenced by both genetic and environmental factors...
December 7, 2018: Journal of Clinical Medicine
Johannes Birtel, Martin Gliem, Elisabeth Mangold, Philipp L Müller, Frank G Holz, Christine Neuhaus, Steffen Lenzner, Diana Zahnleiter, Christian Betz, Tobias Eisenberger, Hanno J Bolz, Peter Charbel Issa
Retinitis pigmentosa (RP) is an inherited degenerative disease causing severe retinal dystrophy and visual impairment mainly with onset in infancy or adolescence. Targeted next-generation sequencing (NGS) has become an efficient tool to encounter the enormous genetic heterogeneity of diverse retinal dystrophies, including RP. To identify disease-causing mutations in unselected, consecutive RP patients, we conducted Sanger sequencing of genes commonly involved in the suspected genetic RP subtype, followed by targeted large-panel NGS if no mutation was identified, or NGS as primary analysis...
2018: PloS One
Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L Kosakovsky Pond, Ben Murrell
Next generation sequencing of viral populations has advanced our understanding of viral population dynamics, the development of drug resistance, and escape from host immune responses. Many applications require complete gene sequences, which can be impossible to reconstruct from short reads. HIV env, the protein of interest for HIV vaccine studies, is exceptionally challenging for long-read sequencing and analysis due to its length, high substitution rate, and extensive indel variation. While long-read sequencing is attractive in this setting, the analysis of such data is not well handled by existing methods...
December 13, 2018: PLoS Computational Biology
Shu-Hsuan Liu, Wei-Chung Cheng
Next generation sequencing (NGS) has become the norm of cancer genomic researches. Large-scale cancer sequencing projects seek to comprehensively uncover mutated genes that confer a selective advantage for cancer cells. Numerous computational algorithms have been developed to find genes that drive cancer based on their patterns of mutation in a patient cohort. It has been noted that the distinct features of driver gene alterations in different subgroups are based on clinical characteristics. Previously, we have developed a database, DriverDB, to integrate all public cancer sequencing data and to identify cancer driver genes according to bioinformatics tools...
2019: Methods in Molecular Biology
Jia Fan, Qian Zhang, Qingxuan Xu, Wenxin Xue, Zongli Han, Jingrui Sun, Julian Chen
Aphidius gifuensis Ashmead is a dominant endoparasitoid of aphids, such as Myzus persicae and Sitobion avenae , and plays an important role in controlling aphids in various habitats, including tobacco plants and wheat in China. A. gifuensis has been successfully applied for the biological control of aphids, especially M. persicae , in green houses and fields in China. The corresponding parasites, as well as its mate-searching behaviors, are subjects of considerable interest. Previous A. gifuensis transcriptome studies have relied on short-read next-generation sequencing (NGS), and the vast majority of the resulting isotigs do not represent full-length cDNA...
2018: Frontiers in Physiology
Allison M Matthews, Ingrid Blydt-Hansen, Basmah Al-Jabri, John Andersen, Maja Tarailo-Graovac, Magda Price, Katherine Selby, Michelle Demos, Mary Connolly, Britt Drögemoller, Casper Shyr, Jill Mwenifumbo, Alison M Elliott, Jessica Lee, Aisha Ghani, Sylvia Stöckler, Ramona Salvarinova, Hilary Vallance, Graham Sinclair, Colin J Ross, Wyeth W Wasserman, Margaret L McKinnon, Gabriella A Horvath, Helly Goez, Clara D van Karnebeek
PURPOSE: The presentation and etiology of cerebral palsy (CP) are heterogeneous. Diagnostic evaluation can be a prolonged and expensive process that might remain inconclusive. This study aimed to determine the diagnostic yield and impact on management of next-generation sequencing (NGS) in 50 individuals with atypical CP (ACP). METHODS: Patient eligibility criteria included impaired motor function with onset at birth or within the first year of life, and one or more of the following: severe intellectual disability, progressive neurological deterioration, other abnormalities on neurological examination, multiorgan disease, congenital anomalies outside of the central nervous system, an abnormal neurotransmitter profile, family history, brain imaging findings not typical for cerebral palsy...
December 13, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Vivek Priy Dave, Tien Anh Ngo, Anna-Karin Pernestig, Diana Tilevik, Krishna Kant, Trieu Nguyen, Anders Wolff, Dang Duong Bang
The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC...
December 12, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
Sanchutha Sathiananthamoorthy, James Malone-Lee, Kiren Gill, Anna Tymon, Trang K Nguyen, Shradha Gurung, Linda Collins, Anthony S Kupelian, Sheela Swamy, Rajvinder Khasriya, David A Spratt, Jennifer L Rohn
Midstream urine culture (MSU) remains the gold standard diagnostic test for confirming urinary tract infection (UTI). We previously showed that patients with chronic lower urinary tract symptoms (LUTS) below the diagnostic cut-off on MSU culture may still harbour bacterial infection, and that their antibiotic treatment was associated with symptom resolution. Here, we evaluated the results of the UK's MSU culture in symptomatic patients and controls. Next, we compared the bacterial enrichment capabilities of the MSU culture with a 50 µl uncentrifuged culture, a 30 ml centrifuged sediment culture, and 16S rRNA gene sequencing...
December 12, 2018: Journal of Clinical Microbiology
Corrie M Whisner, Juan Maldonado, Brandon Dente, Rosa Krajmalnik-Brown, Meg Bruening
BACKGROUND: Modifiable lifestyle factors (e.g. dietary intake and physical activity) are important contributors to weight gain during college. The purpose of this study was to evaluate whether associations exist between body mass index, physical activity, screen time, dietary consumption (fat, protein, carbohydrates, and fiber), and gut microbial diversity during the first year of college. Racially/ethnically diverse college students (n = 82; 61.0% non-white) at a large Southwestern university completed self-reported physical activity and 24-h recall dietary assessments, height and weight measurements, and provided one fecal sample for gut microbiome analysis...
December 12, 2018: BMC Microbiology
Hayase Mizukami, Jun-Dal Kim, Saori Tabara, Weizhe Lu, Chulwon Kwon, Misaki Nakashima, Akiyoshi Fukamizu
Males and females share the same genetic code, but gene expression profile often displays differences between two sexes. Mouse embryonic fibroblasts (MEFs) have been used to experiment as a useful tool to test gene function. They have also been characterized by gender-based differences in expressed genes such as Y-linked Sry or X-linked Hprt. However, there is no report on sex differences in global gene expression. Here, using the next-generation RNA sequencing, we compared the comprehensive transcriptome of MEFs derived from two sexes...
December 12, 2018: Journal of Biochemistry
Alexander Sprygin, Yurii Babin, Yana Pestova, Svetlana Kononova, David B Wallace, Antoinette Van Schalkwyk, Olga Byadovskaya, Vyacheslav Diev, Dmitry Lozovoy, Alexander Kononov
Wide spread incidences of vaccine-like strains of lumpy skin disease virus (LSDV) have recently been reported in a Russian region with a neighboring country that actively vaccinate with a live attenuated LSD vaccine. The use of live-attenuated viruses (LAVs) as vaccines during an active outbreak, creates potential ground for coinfection of hosts and emergence of a strain combining genetic fragments of both parental vaccine and field strains. In this study, we analyse the vaccine-like strain LSDV RUSSIA/Saratov/2017 detected in Saratovskaya oblast, a region sharing border with Kazakhstan...
2018: PloS One
An-Shun Tai, Chien-Hua Peng, Shih-Chi Peng, Wen-Ping Hsieh
Multistage tumorigenesis is a dynamic process characterized by the accumulation of mutations. Thus, a tumor mass is composed of genetically divergent cell subclones. With the advancement of next-generation sequencing (NGS), mathematical models have been recently developed to decompose tumor subclonal architecture from a collective genome sequencing data. Most of the methods focused on single-nucleotide variants (SNVs). However, somatic copy number aberrations (CNAs) also play critical roles in carcinogenesis...
2018: PloS One
Yu-Sheng Chen, Hai-Li Ma, Ying Yang, Wei-Yi Lai, Bao-Fa Sun, Yun-Gui Yang
5-Methylcytosine (m5 C) is a posttranscriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. Many known or novel m5 C sites have been validated by using advanced high-throughput techniques combined with next-generation sequencing (NGS), especially RNA bisulfite sequencing (RNA-BisSeq). Here we introduce an optimized RNA-BisSeq method by using ACT random hexamers to prime the reverse transcription of bisulfite-treated RNA samples to detect the m5 C sites.
2019: Methods in Molecular Biology
Valerie A Arboleda, Rena R Xian
The development of rapid parallel sequencing in the last 20 years has begun a revolution in the field of genetics that is changing nearly all disciplines within biology and medicine. Genomic sequencing has become crucial to the diagnosis and clinical management of patients with constitutional diseases and cancer and has quickly become an integral part of the new era of personalized and precision medicine. The precision medicine initiative, released by the NIH in 2015, has catapulted genomic technologies to the forefront of the practice of medicine and biomedical research...
2019: Methods in Molecular Biology
Lisha Yang, Jiewen Fu, Jingliang Cheng, Chunli Wei, Qi Zhou, Iqra Ijaz, Hongbin Lv, Junjiang Fu
BACKGROUND/AIMS: Familial exudative vitreoretinopathy (FEVR) is a complex hereditary eye disorder characterized by incomplete development of the retinal vasculature, thereby affecting retinal angiogenesis. METHODS: In this study, a Chinese autosomal dominant FEVR pedigree was recruited. Ophthalmic examinations were performed, targeted next-generation sequencing was used to identify the causative gene, and Sanger sequencing was conducted to verify the candidate mutation...
2018: Cellular Physiology and Biochemistry
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