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Next generation sequencing review

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https://www.readbyqxmd.com/read/28721829/ngs-technologies-as-a-turning-point-in-rare-disease-research-diagnosis-and-treatment
#1
Ana Fernández-Marmiesse, Sofía Gouveia, María L Couce
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis...
July 18, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28720679/potential-for-monitoring-gut-microbiota-for-diagnosing-infections-and-graft-versus-host-disease-in-cancer-and-stem-cell-transplant-patients
#2
Andrew Y Koh
BACKGROUND: Gut microbiota, the collective community of microorganisms inhabiting the intestine, have been shown to provide many beneficial functions for the host. Recent advances in next-generation sequencing and advanced molecular biology approaches have allowed researchers to identify gut microbiota signatures associated with disease processes and, in some cases, establish causality and elucidate underlying mechanisms. CONTENT: This report reviews 3 commonly used methods for studying the gut microbiota and microbiome (the collective genomes of the gut microorganisms): 16S rRNA gene sequencing, bacterial group or species-specific quantitative polymerase chain reaction (qPCR), and metagenomic shotgun sequencing (MSS)...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28719387/pediatric-mitochondrial-diseases-and-the-heart
#3
Gregory M Enns
PURPOSE OF REVIEW: Mitochondrial disorders are an increasingly recognized cause of heart dysfunction, with the primary manifestations being cardiomyopathy and conduction defects. This review focuses on the complex genetics of mitochondrial disease and recently discovered conditions that affect mitochondrial function. RECENT FINDINGS: Next-generation sequencing techniques, especially whole-exome sequencing, have led to the discovery of a number of conditions that cause mitochondrial dysfunction and subsequent cardiac abnormalities...
July 17, 2017: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/28715059/the-cost-effectiveness-of-genetic-screening-for-familial-hypercholesterolemia-a-systematic-review
#4
A Rosso, E Pitini, E D'Andrea, A Massimi, C De Vito, C Marzuillo, P Villari
BACKGROUND: Familial hypercholesterolemia (FH) is a genetic disorder that leads to elevated plasma LDL-cholesterol levels and premature coronary heart disease (CHD). An understanding of the mutations responsible for FH and the effectiveness of statins in lowering the risk of CHD in FH patients has increased interest in genetic screening strategies to improve FH diagnosis. In this study, we aimed to evaluate the cost-effectiveness of such strategies. METHODS: We performed a systematic review of full economic evaluations that assessed the cost-effectiveness of FH genetic screening strategies...
September 2017: Annali di Igiene: Medicina Preventiva e di Comunità
https://www.readbyqxmd.com/read/28713573/a-monograph-proposing-the-use-of-canine-mammary-tumours-as-a-model-for-the-study-of-hereditary-breast-cancer-susceptibility-genes-in-humans
#5
REVIEW
Katie Goebel, Nancy D Merner
Canines are excellent models for cancer studies due to their similar physiology and genomic sequence to humans, companion status and limited intra-breed heterogeneity. Due to their affliction to mammary cancers, canines can serve as powerful genetic models of hereditary breast cancers. Variants within known human breast cancer susceptibility genes only explain a fraction of familial cases. Thus, further discovery is necessary but such efforts have been thwarted by genetic heterogeneity. Reducing heterogeneity is key, and studying isolated human populations have helped in the endeavour...
May 2017: Veterinary Medicine and Science
https://www.readbyqxmd.com/read/28712319/primary-liver-cancer-genome-sequencing-translational-implications-and-challenges
#6
Demosthenes E Ziogas, Ioannis D Kyrochristos, Georgios K Glantzounis, Dimitrios Christodoulou, Evangelos Felekouras, Dimitrios H Roukos
The prognosis of primary liver cancer (PLC) remains poor and is explained by the slow progress in understanding the molecular pathways driving tumorigenesis, therapeutic resistance and relapse. For early PLCs, complete surgical resection is the only effective treatment, with sorafenib and, more recently, regorafenib prolonging overall survival by a few months. Areas covered: Application of next-generation sequencing (NGS), including targeted NGS (tNGS), whole-exome sequencing (WES), whole-genome sequencing (WGS) and RNA sequencing (RNAseq), on clinical samples from patients with hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) could aid in comprehending tumorigenesis, genetic and genomic heterogeneity, as well as developing molecular classifications for specialized targeted therapy...
July 17, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28711137/genomics-biology-and%C3%A2-human-illness-advances-in-the-monogenic-autoinflammatory-diseases
#7
REVIEW
Hirotsugu Oda, Daniel L Kastner
The monogenic autoinflammatory diseases are a group of illnesses with prominent rheumatic manifestations that are characterized by genetically determined recurrent sterile inflammation and are thus inborn errors of innate immunity. Molecular targeted therapies against inflammatory cytokines, such as interleukin 1 and tumor necrosis factor, and intracellular cytokine signaling pathways have proved effective in many cases. Emerging next-generation sequencing technologies have accelerated the identification of previously unreported genes causing autoinflammatory diseases...
August 2017: Rheumatic Diseases Clinics of North America
https://www.readbyqxmd.com/read/28710260/big-bang-tumor-growth-and-clonal-evolution
#8
Ruping Sun, Zheng Hu, Christina Curtis
The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution...
July 14, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28710117/genetic-and-epigenetic-drivers-of-neuroendocrine-tumors-net
#9
Annunziata Di Domenico, Tabea Wiedmer, Ilaria Marinoni, Aurel Perren
Neuroendocrine tumors (NET) of the gastrointestinal tract and the lung are a rare and heterogeneous group of tumors. The molecular characterization and the clinical classification of these tumors have been evolving slowly and show differences according to organs of origin. Novel technologies such as next-generation sequencing revealed new molecular aspects of NET over the last years. Notably, whole exome/genome sequencing (WES/WGS) approaches underlined the very low mutation rate of well differentiated NET of all organs compared to other malignancies, while the engagement of epigenetic changes in driving NET evolution is emerging...
July 14, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28705636/a-review-of-bioinformatics-platforms-for-comparative-genomics-recent-developments-of-the-edgar-2-0-platform-and-its-utility-for-taxonomic-and-phylogenetic-studies
#10
J Yu, J Blom, S P Glaeser, S Jaenicke, T Juhre, O Rupp, O Schwengers, S Spänig, A Goesmann
The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics...
July 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28698843/diagnostic-approaches-for-inherited-hemolytic-anemia-in-the-genetic-era
#11
REVIEW
Yonggoo Kim, Joonhong Park, Myungshin Kim
Inherited hemolytic anemias (IHAs) are genetic diseases that present with anemia due to the increased destruction of circulating abnormal RBCs. The RBC abnormalities are classified into the three major disorders of membranopathies, hemoglobinopathies, and enzymopathies. Traditional diagnosis of IHA has been performed via a step-wise process combining clinical and laboratory findings. Nowadays, the etiology of IHA accounts for germline mutations of the responsible genes coding for the structural components of RBCs...
June 2017: Blood Research
https://www.readbyqxmd.com/read/28698797/new-technologies-accelerate-the-exploration-of-non-coding-rnas-in-horticultural-plants
#12
REVIEW
Degao Liu, Ritesh Mewalal, Rongbin Hu, Gerald A Tuskan, Xiaohan Yang
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28696507/the-impact-of-epigenomic-next-generation-sequencing-approaches-on-our-understanding-of-neuropsychiatric-disorders
#13
REVIEW
Anne-Laure Schang, Délara Sabéran-Djoneidi, Valérie Mezger
Patients suffering from psychiatric disorders have a life span burden, which represents an enormous human, family, social, and economical cost. Several concepts have revolutionized our way of appraising neuropsychiatric disorders (NPDs). They result from a combination of genetic factors and environmental insults, and their etiology finds roots in the neurodevelopmental period. As epigenetic mechanisms tightly control brain development, exposure to adverse conditions disturbing the epigenetic landscape of the fetal brain increases the risk of developing NPDs, due to the persistence of abnormal epigenetic signatures, at distance from the initial stimulus...
July 11, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28696069/hcc-associated-single-nucleotide-variants-and-deletions-identified-using-genome-wide-high-throughput-analysis-of-hbv
#14
Wen-Chun Liu, I-Chin Wu, Yen-Chien Lee, Chih-Peng Lin, Ji-Hong Cheng, Yih-Jyh Lin, Chia-Jui Yen, Pin-Nan Cheng, Pei-Fu Li, Yi-Ting Cheng, Pei-Wen Cheng, Koun-Tem Sun, Shu-Ling Yan, Jia-Jhen Lin, Jui-Chu Yang, Kung-Chao Chang, Cheng-Hsun Ho, Vincent S Tseng, Bill Chia-Han Chang, Jaw-Ching Wu, Ting-Tsung Chang
This study investigated hepatitis B virus (HBV) single nucleotide variants (SNVs) and deletion mutations linked with hepatocellular carcinoma (HCC). Ninety-three HCC patients and 108 non-HCC patients were enrolled for HBV genome-wide next-generation sequencing (NGS) analysis. Systemic literature review and meta-analysis were performed to validate NGS-defined HCC-associated SNVs and deletions. The experimental results identified 60 NGS-defined HCC-associated SNVs, including 41 novel SNVs, and their pathogenic frequencies...
July 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28693800/review-of-sequencing-platforms-and-their-applications-in-phaeochromocytoma-and-paragangliomas
#15
REVIEW
Suja Pillai, Vinod Gopalan, Alfred King-Yin Lam
Genetic testing is recommended for patients with phaeochromocytoma (PCC) and paraganglioma (PGL) because of their genetic heterogeneity and heritability. Due to the large number of susceptibility genes associated with PCC/PGL, next-generation sequencing (NGS) technology is ideally suited for carrying out genetic screening of these individuals. New generations of DNA sequencing technologies facilitate the development of comprehensive genetic testing in PCC/PGL at a lower cost. Whole-exome sequencing and targeted NGS are the preferred methods for screening of PCC/PGL, both having precise mutation detection methods and low costs...
August 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28693197/recent-developments-in-predictive-biomarkers-of-pediatric-glioma
#16
Zhengwei Li, Yiyu Yin, Fengli Liu
The presence of certain cancer-related genetic and epigenetic alterations in the tumor affects patient response to specific cancer therapies. The accurate screening of these predictive biomarkers in molecular diagnostics is important since it enables the tailoring of optimal treatment based on molecular characteristics of the tumor. We searched the electronic database PubMed for preclinical as well as clinical controlled trials reporting on various multiple predictors of glioma. It was observed clearly that multiple approaches are evolving and a few of them have also shown promising results...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28690986/next-generation-sequencing-and-array-based-comparative-genomic-hybridization-for-molecular-diagnosis-of-pediatric-endocrine-disorders
#17
REVIEW
Maki Fukami, Mami Miyado
Next-generation sequencing (NGS) and array-based comparative genomic hybridization (array CGH) have enabled us to perform high-throughput mutation screening and genome-wide copy number analysis, respectively. These methods can be used for molecular diagnosis of pediatric endocrine disorders. NGS has determined the frequency and phenotypic variation of mutations in several disease-associated genes. Furthermore, whole exome analysis using NGS has successfully identified several novel causative genes for endocrine disorders...
June 2017: Annals of Pediatric Endocrinology & Metabolism
https://www.readbyqxmd.com/read/28690070/plant-viruses-and-viroids-in-the-united-kingdom-an-analysis-of-first-detections-and-novel-discoveries-from-1980-2014
#18
REVIEW
A Fox, R A Mumford
This review covers 35 years (1980-2014) representing a period of changing land use and agricultural practices in the United Kingdom (UK), which have also witnessed a marked change in the availability and application of new diagnostic technologies. During this period there have been 53 first records of viruses and viroids, of which 36 were first UK findings and a further 17 previously undescribed viruses. Given the challenges in detection and diagnosis of plant viruses, the field of plant virology has been an early adopter of new diagnostic technologies and these data highlight the transition from a reliance on biological, morphological, and serological based identification to the increased application of nucleic acid based detection methods and latterly the emergence of Next-Generation Sequencing...
July 6, 2017: Virus Research
https://www.readbyqxmd.com/read/28689782/the-microbiota-and-autoimmunity-their-role-in-thyroid-autoimmune-diseases
#19
REVIEW
Hedda L Köhling, Sue F Plummer, Julian R Marchesi, Kelly S Davidge, Marian Ludgate
Since the 1970s, the role of infectious diseases in the pathogenesis of Graves' disease (GD) has been an object of intensive research. The last decade has witnessed many studies on Yersinia enterocolitica, Helicobacter pylori and other bacterial organisms and their potential impact on GD. Retrospective, prospective and molecular binding studies have been performed with contrary outcomes. Until now it is not clear whether bacterial infections can trigger autoimmune thyroid disease. Common risk factors for GD (gender, smoking, stress, and pregnancy) reveal profound changes in the bacterial communities of the gut compared to that of healthy controls but a pathogenetic link between GD and dysbiosis has not yet been fully elucidated...
July 6, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28688671/mining-metagenomic-data-sets-for-ancient-dna-recommended-protocols-for-authentication
#20
REVIEW
Felix M Key, Cosimo Posth, Johannes Krause, Alexander Herbig, Kirsten I Bos
While a comparatively young area of research, investigations relying on ancient DNA data have been highly valuable in revealing snapshots of genetic variation in both the recent and the not-so-recent past. Born out of a tradition of single-locus PCR-based approaches that often target individual species, stringent criteria for both data acquisition and analysis were introduced early to establish high standards of data quality. Today, the immense volume of data made available through next-generation sequencing has significantly increased the analytical resolution offered by processing ancient tissues and permits parallel analyses of host and microbial communities...
July 5, 2017: Trends in Genetics: TIG
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