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"next generation sequencing"

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
J L M Van Gennip, C W Boswell, B Ciruna
The etiopathogenesis of idiopathic scoliosis (IS), a highly prevalent spinal deformity that occurs in the absence of obvious congenital or physiological abnormalities, is poorly understood. Although recent zebrafish genetic studies have linked cilia motility and cerebrospinal fluid (CSF) flow defects with scoliosis progression, underlying mechanisms were not identified. Here, we use next-generation sequencing and conditional genetic methodologies to define the spatial and biological origins of spinal curve formation in ptk7 mutant zebrafish, a faithful IS model...
December 2018: Science Advances
Piers Blombery, Ella Thompson, Georgina L Ryland, Rachel Joyce, David J Byrne, Christine Khoo, Stephen Lade, Mark Hertzberg, Greg Hapgood, Paula Marlton, Anand Deva, Geoffrey Lindeman, Stephen Fox, David Westerman, Miles Prince
Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a rare form of T-cell lymphoma that occurs after implantation of breast prostheses. We performed comprehensive next generation sequencing based genomic characterization of 11 cases of BIA-ALCL including sequence variant detection on 180 genes frequently mutated in haematological malignancy, genome-wide copy number assessment, structural variant detection involving the T-cell receptor loci and TRB deep-sequencing. We observed sequence variants leading to JAK/STAT activation in 10 out of 11 patients...
November 16, 2018: Oncotarget
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
Daniel Boloc, Anna Gortat, Jia Qi Cheng-Zhang, Susana García-Cerro, Natalia Rodríguez, Mara Parellada, Jeronimo Saiz-Ruiz, Manolo J Cuesta, Patricia Gassó, Amalia Lafuente, Miquel Bernardo, Sergi Mas
In previous work we developed a pharmacogenetic predictor of antipsychotic (AP) induced extrapyramidal symptoms (EPS) based on four genes involved in mTOR regulation. The main objective is to improve this predictor by increasing its biological plausibility and replication. We re-sequence the four genes using next-generation sequencing. We predict functionality "in silico" of all identified SNPs and test it using gene reporter assays. Using functional SNPs, we develop a new predictor utilizing machine learning algorithms (Discovery Cohort, N = 131) and replicate it in two independent cohorts (Replication Cohort 1, N = 113; Replication Cohort 2, N = 113)...
December 13, 2018: Translational Psychiatry
Benjamin Edginton-White, Pierre Cauchy, Salam A Assi, Sylvia Hartmann, Arthur G Riggs, Stephan Mathas, Peter N Cockerill, Constanze Bonifer
Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported in classical Hodgkin Lymphoma (cHL) that a member of the THE1B class of LTR elements acted as a promoter for the proto-oncogene and growth factor receptor gene CSF1R and that expression of this gene is required for cHL tumour survival. However, to which extent and how such elements participate in globally shaping the unique cHL gene expression programme is unknown...
December 13, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Ching-Hon Pui, Kim E Nichols, Jun J Yang
Advances in genomic research and risk-directed therapy have led to improvements in the long-term survival and quality of life outcomes of patients with childhood acute lymphoblastic leukaemia (ALL). The application of next-generation sequencing technologies, especially transcriptome sequencing, has resulted in the identification of novel molecular subtypes of ALL with prognostic and therapeutic implications, as well as cooperative mutations that account for much of the heterogeneity in clinical responses observed among patients with specific ALL subtypes...
December 13, 2018: Nature Reviews. Clinical Oncology
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
Hairong Wang, Yun Yang, Jieqiong Zhou, Jiangxia Cao, Xuelian He, Long Li, Shuyang Gao, Bing Mao, Ping Tian, Aifen Zhou
RATIONALE: Epidermolysis bullosa (EB) refers to a group of rare inherited mechanobullous disorders that present with great clinical and genetic heterogeneity. Its severity ranges from mild blistering to life-threatening. However, the clinical symptoms of different types of EB overlap significantly, especially at an early stage. Thus it is important to clarify the diagnosis for prognostic implications, patient management, and genetic counseling. PATIENT CONCERNS: Here, we report a 10-day-old male neonate from a nonconsanguineous Chinese family...
December 2018: Medicine (Baltimore)
Tao Hong, Yupeng Yan, Jingwei Li, Ivan Radovanovic, Xiangyuan Ma, Yang W Shao, Jiaxing Yu, Yongjie Ma, Peng Zhang, Feng Ling, Shuchen Huang, Hongqi Zhang, Yibo Wang
Brain and spinal arteriovenous malformations are congenital lesions causing intracranial haemorrhage or permanent disability especially in young people. We investigated whether the vast majority or all brain and spinal arteriovenous malformations are associated with detectable tumour-related somatic mutations. In a cohort of 31 patients (21 with brain and 10 with spinal arteriovenous malformations), tissue and paired blood samples were analysed with ultradeep next generation sequencing of a panel of 422 common tumour genes to identify the somatic mutations...
December 12, 2018: Brain: a Journal of Neurology
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
Ivana Kašubová, Veronika Holubeková, Katarína Janíková, Barbora Váňová, Zuzana Sňahničanová, Michal Kalman, Lukáš Plank, Zora Lasabová
The development of the new technologies such as the next-generation sequencing (NGS) makes more accessible the diagnosis of genetically heterogeneous diseases such as Lynch syndrome (LS). LS is one of the most common hereditary form of colorectal cancer. This autosomal dominant inherited disorder is caused by deleterious germline mutations in one of the mismatch repair (MMR) genes - MLH1, MSH2, MSH6 or PMS2, or the deletion in the EPCAM gene. These mutations eventually result in microsatellite instability (MSI), which can be easily tested in tumor tissue...
2018: Acta Medica (Hradec Králové)
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
Shiho Takeuchi, Shujiro Okuda
In Japan, the National Cancer Center and university hospitals have initiated next-generation sequencing-based in vitro diagnostic testing for cancer patients as a method of clinical sequencing. Based on the molecular alterations detected, physicians can provide approved targeted therapy and access to investigational drugs for cancer patients. However, interpretation of the clinical significance of genomic alterations remains the most severe bottleneck of precision medicine in cancer. Although many research institutes in the United States are developing knowledge bases for interpretation of the tumor alterations and clinical decisions, these knowledge bases are unsuited as sources of reference in Japan due to differences in the information on approved drugs and implementation of clinical trials...
December 12, 2018: International Journal of Clinical Oncology
Chia-Yi Hsu, Tsung-Hua Hsieh, Tze-Kiong Er, Hung-Sheng Chen, Ching-Chou Tsai, Eing-Mei Tsai
Ovarian cancer is the one of the most lethal gynecological cancer types. MicroRNAs (miRs) are noncoding RNAs that modulate the translation of their target mRNAs via binding to a complementary sequence in the target 3' untranslated region, and the dysregulation of certain miRs has been demonstrated to contribute to cancer progression. In this regard, the current study extended our previous work and used next‑generation sequencing data to search for upstream regulators of genetic alterations that are common in ovarian cancer, as well as the miRs that are involved in controlling the expression of these regulators...
October 9, 2018: Oncology Reports
Maxime Gaudin, Christelle Desnues
This review describes target-enrichment approaches followed by next generation sequencing and their recent application to the research and diagnostic field of modern and past infectious human diseases caused by viruses, bacteria, parasites and fungi.
2018: Frontiers in Microbiology
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