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https://www.readbyqxmd.com/read/29222953/bacterial-community-changes-in-copper-and-pex-drinking-water-pipeline-biofilms-under-extra-disinfection-and-magnetic-water-treatment
#1
Jenni Inkinen, Balamuralikrishna Jayaprakash, Merja Ahonen, Tarja Pitkänen, Riika Mäkinen, Anna Pursiainen, Jorge W Santo Domingo, Heidi Salonen, Michael Elk, Minna M Keinänen-Toivola
AIMS: To study stability of biofilms and water quality in pilot scale drinking water copper and PEX pipes in changing conditions (extra disinfection, magnetic water treatment MWT). METHODS AND RESULTS: Next-generation sequencing (NGS) of 16S ribosomal RNA genes (rDNA) to describe total bacterial community and ribosomal RNA (rRNA) to describe active bacterial members in addition to traditional microbiological methods were applied. Biofilms from control copper and PEX pipes shared same most abundant bacteria (Methylobacterium spp...
December 9, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29222064/evolution-in-the-amphi-atlantic-tropical-genus-guibourtia-fabaceae-detarioideae-combining-ngs-phylogeny-and-morphology
#2
Félicien Tosso, Olivier J Hardy, Jean-Louis Doucet, Kasso Daïnou, Esra Kaymak, Jérémy Migliore
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29221448/next-generation-sequencing-recent-applications-to-the-analysis-of-colorectal-cancer
#3
REVIEW
Filippo Del Vecchio, Valentina Mastroiaco, Antinisca Di Marco, Chiara Compagnoni, Daria Capece, Francesca Zazzeroni, Carlo Capalbo, Edoardo Alesse, Alessandra Tessitore
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics...
December 8, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29220350/deep-sequencing-of-near-full-length-hiv-1-genomes-from-plasma-identifies-circulating-subtype-c-and-infrequent-occurrence-of-ac-recombinant-form-in-southern-india
#4
Shuba Varshini Alampalli, Michael M Thomson, Raghavan Sampathkumar, Karthi Sivaraman, Anto Jesuraj U K J, Chirag Dhar, George D Souza, Neil Berry, Annapurna Vyakarnam
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/29218886/clingen-cancer-somatic-working-group-standardizing-and-democratizing-access-to-cancer-molecular-diagnostic-data-to-drive-translational-research
#5
Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew Mccoy, Malachi Griffith, Obi L Griffith, Peter Mcgarvey, Shashikant Kulkarni
A growing number of academic and community clinics are conducting genomic testing to inform treatment decisions for cancer patients (1). In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing (2). The increasing availability and decreasing cost of tumor genomic profiling means that physicians can now make treatment decisions armed with patient-specific genetic information. Accumulating research in the cancer biology field indicates that there is significant potential to improve cancer patient outcomes by effectively leveraging this rich source of genomic data in treatment planning (3)...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218053/marker-development-for-phylogenomics-the-case-of-orobanchaceae-a-plant-family-with-contrasting-nutritional-modes
#6
Xi Li, Baohai Hao, Da Pan, Gerald M Schneeweiss
Phylogenomic approaches, employing next-generation sequencing (NGS) techniques, have revolutionized systematic and evolutionary biology. Target enrichment is an efficient and cost-effective method in phylogenomics and is becoming increasingly popular. Depending on availability and quality of reference data as well as on biological features of the study system, (semi-)automated identification of suitable markers will require specific bioinformatic pipelines. Here, we established a highly flexible bioinformatic pipeline, BaitsFinder, to identify putative orthologous single copy genes (SCGs) and to construct bait sequences in a single workflow...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29216377/peachvar-db-a-curated-collection-of-genetic-variations-for-the-interactive-analysis-of-peach-genome-data
#7
Marco Cirilli, Tiziano Flati, Silvia Gioiosa, Ilario Tagliaferri, Angelo Ciacciulli, Zhongshan Gao, Stefano Gattolin, Filippo Geuna, Francesco Maggi, Paolo Bottoni, Laura Rossini, Daniele Bassi, Tiziana Castrignanò, Giovanni Chillemi
Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalogue of genetic variants present in peach (P. persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Reads Archive (SRA)...
December 4, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#8
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29214758/comparison-of-four-human-papillomavirus-genotyping-methods-next-generation-sequencing-inno-lipa-electrochemical-dna-chip-and-nested-pcr
#9
Pornjarim Nilyanimit, Jira Chansaenroj, Witthaya Poomipak, Kesmanee Praianantathavorn, Sunchai Payungporn, Yong Poovorawan
BACKGROUND: Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. METHODS: Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS)...
March 2018: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/29214754/utility-of-conventional-culture-and-maldi-tof-ms-for-identification-of-microbial-communities-in-bronchoalveolar-lavage-fluid-in-comparison-with-the-gs-junior-next-generation-sequencing-system
#10
Ji Yeon Sung, Younjee Hwang, Mi Hwa Shin, Moo Suk Park, Sang Hoon Lee, Dongeun Yong, Kyungwon Lee
BACKGROUND: Diverse microbiota exist in the lower respiratory tract. Although next generation sequencing (NGS) is the most widely used microbiome analysis technique, it is difficult to implement NGS in clinical microbiology laboratories. Therefore, we evaluated the performance of conventional culture methods together with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying microbiota in bronchoalveolar lavage (BAL) fluid. METHODS: BAL fluid samples (n=27) were obtained from patients undergoing diagnostic bronchoscopy for lung mass evaluation...
March 2018: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/29214632/thorough-analysis-of-unorthodox-abo-deletions-called-by-the-1000-genomes-project
#11
M Möller, Å Hellberg, M L Olsson
BACKGROUND AND OBJECTIVES: ABO remains the clinically most important blood group system, but despite earlier extensive research, significant findings are still being made. The vast majority of catalogued ABO null alleles are based on the c.261delG polymorphism. Apart from c.802G>A, other mechanisms for O alleles are rare. While analysing the data set from the 1000 Genomes (1000G) project, we encountered two previously uncharacterized deletions, which needed further exploration. MATERIALS AND METHODS: The Erythrogene database, complemented with bioinformatics software, was used to analyse ABO in 2504 individuals from 1000G...
December 6, 2017: Vox Sanguinis
https://www.readbyqxmd.com/read/29212833/personalized-cancer-therapy-leveraging-a-knowledge-base-for-clinical-decision-making
#12
Ecaterina Ileana Dumbrava, Funda Meric-Bernstam
The next-generation sequencing (NGS), also known as massively parallel sequencing, is rapidly being incorporated into oncology practice. With increasing numbers of genes tested, interpretation of genomic reports and selecting treatments based on the tumor's genomic analysis becomes more and more complicated for the treating oncologist. To help guide personalized treatments in oncology, The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy (IPCT) at MD Anderson Cancer Center has developed a knowledge base, available at https://personalizedcancertherapy...
December 6, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29212777/detection-and-monitoring-of-circulating-tumor-dna-in-adrenocortical-carcinoma
#13
Simon Garinet, Juliette Nectoux, Mario Neou, Eric Pasmant, Anne Jouinot, Mathilde Sibony, Lucie Orhant, Juliana Pipoli da Fonseca, Karine Hecale-Perlemoine, Leopoldine Bricaire, Lionel Groussin, Olivier Soubrane, Bertrand Dousset, Rossella Libé, Franck Letourneur, Jerome Bertherat, Guillaume Assié
Adrenocortical carcinomas (ACC) are aggressive tumors with limited prognostic and follow-up biomarkers. Circulating tumor DNA (ctDNA) is an emerging biomarker, now used for several cancer types. This study aimed to reliably detect and quantify ctDNA in ACC patients; to identify parameters impacting detection of ctDNA. A prospective monocentric study conducted in Cochin Hospital and Cochin Institute, Paris, France. Eleven ACC patients were included with either primary tumor or relapse or metastases from 2015 to 2016...
December 6, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29212165/assessment-of-pancreatic-neuroendocrine-tumor-cytologic-genotype-diversity-to-guide-personalized-medicine-using-a-custom-gastroenteropancreatic-next-generation-sequencing-panel
#14
Ferga C Gleeson, Jesse S Voss, Benjamin R Kipp, Sarah E Kerr, John S Van Arnam, John R Mills, Cherisse A Marcou, Amber R Schneider, Zheng Jin Tu, Michael R Henry, Michael J Levy
Background: Recent genetic studies have highlighted that alterations in MEN1, chromatin remodeling genes, and mammalian target of rapamycin (mTOR) pathway genes are the most frequent molecular events identified in pancreas neuroendocrine tumors (pNETs). The prognostic or predictive impact of these biomarkers and other less frequently observed aberrations, i.e. PTEN, TSC2 and PIK3CA are relatively unknown. The aims of this targeted next generation sequencing (NGS) study were to assess tumor cytology genotype diversity, to survey for potential adverse prognostic biomarkers and the prevalence of mTOR pathway variants...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29212164/targeted-sequencing-of-established-and-candidate-colorectal-cancer-genes-in-the-colon-cancer-family-registry-cohort
#15
Leon Raskin, Yan Guo, Liping Du, Mark Clendenning, Christophe Rosty, Noralane M Lindor, Stephen B Gruber, Daniel D Buchanan
The underlying genetic cause of colorectal cancer (CRC) can be identified for 5-10% of all cases, while at least 20% of CRC cases are thought to be due to inherited genetic factors. Screening for highly penetrant mutations in genes associated with Mendelian cancer syndromes using next-generation sequencing (NGS) can be prohibitively expensive for studies requiring large samples sizes. The aim of the study was to identify rare single nucleotide variants and small indels in 40 established or candidate CRC susceptibility genes in 1,046 familial CRC cases (including both MSS and MSI-H tumor subtypes) and 1,006 unrelated controls from the Colon Cancer Family Registry Cohort using a robust and cost-effective DNA pooling NGS strategy...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29210102/the-use-of-droplet-digital-pcr-in-liquid-biopsies-a-highly-sensitive-technique-for-myd88-p-l265p-detection-in-cerebrospinal-fluid
#16
Laura S Hiemcke-Jiwa, Monique C Minnema, Joyce H Radersma-van Loon, N Mehdi Jiwa, Mirthe de Boer, Roos J Leguit, Roel A de Weger, Manon M H Huibers
The gold standard for diagnosis of central nervous system lymphomas still regards a stereotactic brain biopsy, with the risk of major complications for the patient. As tumor cells can be detected in cerebrospinal fluid (CSF), CSF analysis can be used as an alternative. In this respect, mutation analysis in CSF can be of added value to other diagnostic parameters such a cytomorphology and clonality analysis. A well-known example of targeted mutation analysis entails MYD88 p.(L265P) detection, which is present in the majority of Bing Neel syndrome and primary central nervous system lymphoma (PCNSL) patients...
December 6, 2017: Hematological Oncology
https://www.readbyqxmd.com/read/29209992/cost-effectiveness-of-karyotyping-chromosomal-microarray-analysis-and-targeted-next-generation-sequencing-of-patients-with-unexplained-global-developmental-delay-or-intellectual-disability
#17
Yonghong Li, Lori A Anderson, Edward I Ginns, James J Devlin
BACKGROUND: Genetic diagnosis of unexplained global developmental delay and intellectual disability (GDD/ID) often ends the diagnostic odyssey and can lead to changes in clinical management. OBJECTIVE: The objective of this study was to investigate the cost effectiveness of testing scenarios involving several methods used to diagnose GDD/ID: karyotyping, chromosomal microarray analysis (CMA), and targeted next-generation sequencing (NGS). METHODS: We used decision-tree models to estimate the number of genetic diagnoses, the cost from a payers' perspective in the USA, and the incremental cost per additional genetic diagnosis...
December 5, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/29209898/clinical-application-of-next-generation-sequencing-in-hereditary-spinocerebellar-ataxia-increasing-the-diagnostic-yield-and-broadening-the-ataxia-spasticity-spectrum-a-retrospective-analysis
#18
REVIEW
Daniele Galatolo, Alessandra Tessa, Alessandro Filla, Filippo M Santorelli
One of the hardest challenges in medical genetics is to reach a molecular diagnosis in the presence of rare brain disorders. Hereditary spinocerebellar ataxia (HA), characterized by high clinical and genetic heterogeneity, is among the diseases that present this challenge. HA can have features overlapping with those of other neurological diseases, especially hereditary spastic paraplegia (HSP), as routine clinical application of next generation sequencing (NGS) has confirmed. This article reviews different NGS methods applied in heterogeneous cohorts of patients with suspected HA and suggests that exome sequencing should be considered the first-tier genetic approach in this setting...
December 6, 2017: Neurogenetics
https://www.readbyqxmd.com/read/29209042/analysis-of-the-genomic-landscape-of-multiple-myeloma-highlights-novel-prognostic-markers-and-disease-subgroups
#19
N Bolli, G Biancon, M Moarii, S Gimondi, Y Li, C de Philippis, F Maura, V Sathiaseelan, Y-T Tai, L Mudie, S O'Meara, K Raine, J W Teague, A P Butler, C Carniti, M Gerstung, T Bagratuni, E Kastritis, M Dimopoulos, P Corradini, K Anderson, P Moreau, S Minvielle, P J Campbell, E Papaemmanuil, H Avet-Loiseau, N C Munshi
In multiple myeloma, next generation sequencing (NGS) has expanded our knowledge of genomic lesions, and highlighted a dynamic and heterogeneous composition of the tumor. Here, we used NGS to characterize the genomic landscape of 418 multiple myeloma cases at diagnosis and correlate this with prognosis and classification. Translocations and copy number changes (CNAs) had a preponderant contribution over gene mutations in defining the genotype and prognosis of each case. Known and novel independent prognostic markers were identified in our cohort of proteasome inhibitor and IMiD-treated patients with long follow-up, including events with context-specific prognostic value, such as deletions of the PRDM1 gene...
December 6, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29206226/merging-ft-ir-and-ngs-for-simultaneous-phenotypic-and-genotypic-identification-of-pathogenic-candida-species
#20
Claudia Colabella, Laura Corte, Luca Roscini, Volha Shapaval, Achim Kohler, Valeria Tafintseva, Carlo Tascini, Gianluigi Cardinali
The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments...
2017: PloS One
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