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https://www.readbyqxmd.com/read/28724077/physical-map-of-the-short-arm-of-bread-wheat-chromosome-3d
#1
Kateřina Holušová, Jan Vrána, Jan Šafář, Hana Šimková, Barbora Balcárková, Zeev Frenkel, Benoit Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel, Jan Bartoš
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724065/comparative-mapping-and-targeted-capture-sequencing-of-the-gametocidal-loci-in-aegilops-sharonensis
#2
Surbhi Grewal, Laura-Jayne Gardiner, Barbora Ndreca, Emilie Knight, Graham Moore, Ian P King, Julie King
Gametocidal (Gc) chromosomes or elements in species such as Eig are preferentially transmitted to the next generation through both the male and female gametes when introduced into wheat ( L.). Furthermore, any genes, such as genes that control agronomically important traits, showing complete linkage with Gc elements, are also transmitted preferentially to the next generation without the need for selection. The mechanism for the preferential transmission of the Gc elements appears to occur by the induction of extensive chromosome damage in any gametes that lack the Gc chromosome in question...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723969/matrixlysis-an-improved-sample-preparation-method-for-recovery-of-mycobacteria-from-animal-tissue-material
#3
Christoph Leth, Ashok Varadharajan, Patrick Mester, Marlis Fischaleck, Peter Rossmanith, Friedrich Schmoll, Maria Fink
Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, is the main causative agent of bovine tuberculosis in alpine regions. Bacterial culture is the gold standard in bovine tuberculosis diagnostic but takes up to twelve weeks. This increases the time and costs for stocks affected with bovine tuberculosis. Hence this study focused on the implementation of a fast and precise mycobacterial detection method and compared it with currently used methods. Matrix lysis is a chemical lysis using high concentrations of urea to solubilize bovine and red deer tissue and was used to detect even smallest amounts or non-visible lesions of mycobacteria...
2017: PloS One
https://www.readbyqxmd.com/read/28723968/new-library-construction-method-for-single-cell-genomes
#4
Larry Xi, Alexander Belyaev, Sandra Spurgeon, Xiaohui Wang, Haibiao Gong, Robert Aboukhalil, Richard Fekete
A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments...
2017: PloS One
https://www.readbyqxmd.com/read/28723942/comparative-analysis-of-vaginal-microbiota-sampling-using-16s-rrna-gene-analysis
#5
Seppo Virtanen, Ilkka Kalliala, Pekka Nieminen, Anne Salonen
BACKGROUND: Molecular methods such as next-generation sequencing are actively being employed to characterize the vaginal microbiota in health and disease. Previous studies have focused on characterizing the biological variation in the microbiota, and less is known about how factors related to sampling contribute to the results. Our aim was to investigate the impact of a sampling device and anatomical sampling site on the quantitative and qualitative outcomes relevant for vaginal microbiota research...
2017: PloS One
https://www.readbyqxmd.com/read/28723901/2b-rad-genotyping-for-population-genomic-studies-of-chagas-disease-vectors-rhodnius-ecuadoriensis-in-ecuador
#6
Luis E Hernandez-Castro, Marta Paterno, Anita G Villacís, Björn Andersson, Jaime A Costales, Michele De Noia, Sofía Ocaña-Mayorga, Cesar A Yumiseva, Mario J Grijalva, Martin S Llewellyn
BACKGROUND: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses...
July 19, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28723342/molecular-analysis-of-circulating-free-dna-from-lung-cancer-patients-in-routine-laboratory-practice-a-cross-platform-comparison-of-three-different-molecular-methods-for-mutation-detection
#7
Stephan Bartels, Sascha Persing, Britta Hasemeier, Elisa Schipper, Hans Kreipe, Ulrich Lehmann
Cell-free DNA (cfDNA), which is isolated from blood plasma, represents a noninvasive source for the detection of mutations conferring resistance against epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in non-small-cell lung cancer patients. In advanced disease stages, performing regular biopsies is often not possible because of the general health condition of the patients. Furthermore, a biopsy of a single tumor lesion or metastasis may not reflect the heterogeneous genotype of the tumor and its metastases...
July 16, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28722833/targeted-next-generation-sequencing-using-a-multigene-panel-in-myeloid-neoplasms-implementation-in-clinical-diagnostics
#8
B Maes, J Willemse, A Broekmans, R Smets, B Cruys, N Put, V Madoe, M Janssen, O Soepenberg, G Bries, I Vrelust, R Achten, K Van Pelt, K Buvé, K Theunissen, V Peeters, G Froyen
INTRODUCTION: Detection of mutations in patients with myeloid neoplasms (MNs) has shown great potential for diagnostic and prognostic purposes. Next-generation sequencing (NGS) is currently implemented for the diagnostic profiling of the four major MN subgroups. METHODS: First, we validated the targeted NGS approach using the TruSight Myeloid panel. Next, we screened 287 patients with a clinical suspicion of MN and 61 follow-up patients with documented MN. RESULTS: Validation of the NGS workflow resulted in maximal precision, accuracy, sensitivity, and specificity for gene variants with an allele frequency of at least 5% and a minimal read depth of 300...
July 19, 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28722430/multi-amplified-sensing-of-microrna-by-a-small-dna-fragment-driven-enzymatic-cascade-reaction
#9
Eunjung Kim, Philip D Howes, Spencer W Crowder, Molly M Stevens
Combining technological developments such as nanomaterials, DNA nanotechnology, and functional enzymes has great potential to facilitate next generation high performance molecular diagnostic systems. In this work, we describe a microRNA (miRNA) detection assay that combines target recycling and isothermal amplification in an elegantly designed enzyme-mediated cascade reaction. Target recycling is driven by the action of duplex-specific nuclease (DSN), resulting in highly amplified translation of input miRNA to short output DNA fragments...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722367/-next-generation-sequencing-a-diagnostic-tool-for-inherited-immune-defects
#10
Stéphanie Droz-Georget, Orbicia Riccio, Béryl Royer-Bertrand, Andrea Superti-Furga, Fabio Candotti
Establishing the definitive diagnosis in the case of inherited immune defects (IID) is often challenging because the clinical features can be heterogeneous, atypical and overlapping different disease entities. The next generation sequencing technology (NGS) allows identifying genetic variants that are responsible for the observed clinical presentations. The use of NGS applied to the genes mutated in IIDs or known to be involved in the development, differentiation and regulation of the immune system allows to target hundreds of relevant genes in well characterized patients suspected of carrying inherited immune defects...
April 5, 2017: Revue Médicale Suisse
https://www.readbyqxmd.com/read/28722212/active-human-papillomavirus-involvement-in-barrett-s-dysplasia-and-oesophageal-adenocarcinoma-is-characterized-by-wild-type-p53-and-aberrations-of-the-retinoblastoma-protein-pathway
#11
Shanmugarajah Rajendra, Tao Yang, Wei Xuan, Prateek Sharma, Darren Pavey, Cheong Soon Lee, Son Le, Josephine Collins, Bin Wang
We have previously demonstrated that transcriptionally active high-risk HPV (hr-HPV) is strongly incriminated in Barrett's dysplasia (BD) and oesophageal adenocarcinoma (OAC) using mainly fresh frozen tissue. This study aimed to identify biomarkers of active HPV infection in Barrett's metaplasia, (BM)/BD/OAC by immunohistochemical staining (IHC) of formalin-fixed paraffin embedded (FFPE) tissue for aberrations of p53 and the retinoblastoma (pRb) pathway which are targets for the viral oncoproteins, E6/E7 respectively...
July 19, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28721829/ngs-technologies-as-a-turning-point-in-rare-disease-research-diagnosis-and-treatment
#12
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/28721808/molecular-tests-for-the-choice-of-cancer-therapy
#13
Anna P Sokolenko, Evgeny N Imyanitov
There are over a dozen of approved cancer drugs, whose administration is tailored to predictive laboratory tests. The examples include estrogen and progesterone receptor status determination for the use of endocrine therapy, HER2 assessment for the administration of HER2-targeting agents, EGFR and ALK gene testing for lung cancer treatment, BRAF analysis in melanoma, etc. While first predictive tests relied on relatively easy laboratory procedures, more recent developments require rather sophisticated assays...
July 19, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28721485/non-additive-and-epistatic-effects-of-hla-polymorphisms-contributing-to-risk-of-adult-glioma
#14
Chenan Zhang, Adam J de Smith, Ivan V Smirnov, John K Wiencke, Joseph L Wiemels, John S Witte, Kyle M Walsh
Although genome-wide association studies have identified several susceptibility loci for adult glioma, little is known regarding the potential contribution of genetic variation in the human leukocyte antigen (HLA) region to glioma risk. HLA associations have been reported for various malignancies, with many studies investigating selected candidate HLA polymorphisms. However, no systematic analysis has been conducted in glioma patients, and no investigation into potential non-additive effects has been described...
July 18, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28721353/hepatitis-e-virus-associated-meningoencephalitis-in-a-lung-transplant-recipient-diagnosed-by-clinical-metagenomic-sequencing
#15
Jamie A Murkey, Kara W Chew, Margrit Carlson, Chelsea L Shannon, Deepika Sirohi, Hannah A Sample, Michael R Wilson, Paul Vespa, Romney M Humphries, Steve Miller, Jeffrey D Klausner, Charles Y Chiu
Hepatitis E virus (HEV) infection uncommonly causes chronic hepatitis and neurologic disease. We describe a case of genotype 3a HEV meningoencephalitis diagnosed by metagenomic next-generation sequencing, illustrating the power of an unbiased molecular approach to microbial testing and the first reported case of HEV infection presumably acquired through lung transplantation.
2017: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/28721068/patients-harboring-alk-rearrangement-adenocarcinoma-after-acquired-resistance-to-crizotinib-and-transformation-to-small-cell-lung-cancer-a-case-report
#16
You-Cai Zhu, Xing-Hui Liao, Wen-Xian Wang, Chun-Wei Xu, Wu Zhuang, Li-Hua Zhong, Kai-Qi Du, Yan-Ping Chen, Gang Chen, Mei-Yu Fang
Anaplastic lymphoma kinase (ALK) rearrangement responds to ALK tyrosine kinase inhibitors (TKIs) in lung cancer. Many cases ultimately acquire resistance to crizotinib. Resistance, including ALK-dominant or ALK non-dominant, mechanisms have been described. Transformation to small-cell lung cancer is rare. Herein, we report a 49-year-old man diagnosed with adenocarcinoma, who was negative for EGFR and ALK genes as detected by reverse transcription polymerase chain reaction, and was treated with crizotinib. A new biopsy showed a small-cell lung cancer after disease progression...
2017: OncoTargets and Therapy
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
#17
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/28720677/synthetic-circulating-cell-free-dna-as-quality-control-materials-for-somatic-mutation-detection-in-liquid-biopsy-for-cancer
#18
Rui Zhang, Rongxue Peng, Ziyang Li, Peng Gao, Shiyu Jia, Xin Yang, Jiansheng Ding, Yanxi Han, Jiehong Xie, Jinming Li
BACKGROUND: Detection of somatic genomic alterations in tumor-derived cell-free DNA (cfDNA) in the plasma is challenging owing to the low concentrations of cfDNA, variable detection methods, and complex workflows. Moreover, no proper quality control materials are available currently. METHODS: We developed a set of synthetic cfDNA quality control materials (SCQCMs) containing spike-in cfDNA on the basis of micrococcal nuclease digestion carrying somatic mutations as simulated cfDNA and matched genomic DNA as genetic background to emulate paired tumor-normal samples in real clinical tests...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28720120/interrogating-the-unsequenceable-genomic-trinucleotide-repeat-disorders-by-long-read-sequencing
#19
Qian Liu, Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang
Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28720077/hemolytic-uremic-syndrome-as-the-presenting-manifestation-of-wt1-mutation-and-denys-drash-syndrome-a-case-report
#20
Joseph L Alge, Scott E Wenderfer, John Hicks, Mir Reza Bekheirnia, Deborah A Schady, Jamey S Kain, Michael C Braun
BACKGROUND: Hemolytic uremic syndrome (HUS) can occur as a primary process due to mutations in complement genes or secondary to another underlying disease. HUS sometimes occurs in the setting of glomerular diseases, and it has been described in association with Denys-Drash syndrome (DDS), which is characterized by the triad of abnormal genitourinary development; a pathognomonic glomerulopathy, diffuse mesangial sclerosis; and the development of Wilms tumor. CASE PRESENTATION: We report the case of a 46, XX female infant who presented with HUS and biopsy-proven thrombotic microangiopathy...
July 18, 2017: BMC Nephrology
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