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https://www.readbyqxmd.com/read/28813642/buccal-swab-genomic-dna-fragmentation-predicts-likelihood-of-successful-hla-genotyping-by-next-generation-sequencing
#1
Maureen C Montgomery, Rosanne Petroria, Eric T Weimer
Many clinical human leukocyte antigen (HLA) laboratories are adopting next-generation sequencing (NGS) technology for HLA genotyping. There have been several reports of the cost-benefit and reduction in turn-around-time provided by NGS. Ninety-six percent of buccal swabs and peripheral blood samples had reportable HLA genotyping by NGS. The HLA loci most likely to fail genotyping from buccal swabs were DQB1, DPB1, and DPA1. Successful buccal swab samples had significantly less genomic DNA fragmentation compared to buccal swab samples that were unsuccessful...
August 13, 2017: Human Immunology
https://www.readbyqxmd.com/read/28811656/phageterm-a-tool-for-fast-and-accurate-determination-of-phage-termini-and-packaging-mechanism-using-next-generation-sequencing-data
#2
Julian R Garneau, Florence Depardieu, Louis-Charles Fortier, David Bikard, Marc Monot
The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811564/computational-identification-of-y-linked-markers-and-genes-in-the-grass-carp-genome-by-using-a-pool-and-sequence-method
#3
Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811555/identification-of-novel-micrornas-in-the-sheep-heart-and-their-regulation-in-heart-failure
#4
Lee Lee Wong, Miriam T Rademaker, Eng Leng Saw, Kar Sheng Lew, Leigh J Ellmers, Christopher J Charles, Arthur Mark Richards, Peipei Wang
Study of microRNA (miRNAs) using sheep models is limited due to lack of miRNA information. We therefore investigated oar-miRNAs and their regulation in an ovine model of heart failure (HF). Left ventricular (LV) tissue was collected from normal (Cont), HF (LV pacing @ ~220bpm for 13-days) and HF-recovery sheep (HF-R, 26-days after pacing cessation). MiRNA expression was profiled using next-generation sequencing (NGS) and miRNA array, and validated by stem-loop qPCR. Detected sequences were mapped against the ovine genome (Oar v4...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810845/a-bioinformatics-approach-for-identifying-transgene-insertion-sites-using-whole-genome-sequencing-data
#5
Doori Park, Su-Hyun Park, Yong Wook Ban, Youn Shic Kim, Kyoung-Cheul Park, Nam-Soo Kim, Ju-Kon Kim, Ik-Young Choi
BACKGROUND: Genetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms...
August 15, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28809760/the-milestone-of-non-invasive-prenatal-identification-of-chromosomal-abnormalities-in-fetal-trophoblasts-recovered-from-maternal-blood
#6
Jaime Garcia-Heras
Two recent studies demonstrated that array CGH and NGS allow identification of chromosomal abnormalities in fetal trophoblasts circulating in maternal blood. This remarkable breakthrough paves the way for an improved assay that supersedes the performance of non-invasive prenatal testing (NIPT) in cell-free fetal DNA. Furthermore, it is foreseeable to expand the use of this new genomic analysis in trophoblasts to uncover single gene mutations of clinical significance prenatally.
2017: Journal of the Association of Genetic Technologists
https://www.readbyqxmd.com/read/28809015/systems-biology-analyses-in-chicken-workflow-for-transcriptome-and-chip-seq-analyses-using-the-chicken-skin-paradigm
#7
Yung-Chih Lai, Randall B Widelitz, Cheng-Ming Chuong
With advances in molecular biology, various biological phenomena can now be explored at higher resolution using mRNA sequencing (RNA-Seq) and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), two powerful high-throughput next-generation sequencing (NGS) technologies. While methods are used widely in mouse, human, etc., less information is available in other animals, such as the chicken. Here we assemble a workflow of the RNA-Seq and ChIP-Seq analyses for the chicken studies using chicken skin appendage tissue as an example...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28807936/genomic-alterations-in-circulating-tumor-dna-from-diverse-cancer-patients-identified-by-next-generation-sequencing
#8
Maria Schwaederle, Ranajoy Chattopadhyay, Shumei Kato, Paul T Fanta, Kimberly C Banks, In Sil Choi, David E Piccioni, Sadakatsu Ikeda, AmirAli Talasaz, Richard B Lanman, Lyudmila Bazhenova, Razelle Kurzrock
Non-invasive genomic profiling of tumors may be possible with next-generation sequencing (NGS) of blood-derived circulating tumor DNA (ctDNA), but proof of concept in a large cohort <p>of patients with diverse cancers has yet to be reported. Here we report the results of an analysis of plasma-derived ctDNA from 670 patients with diverse cancers.</p> The tumors represented in the patient cohort were mainly gastrointestinal (31.8%), brain (22.7%) or lung (20.7%). ctDNA obtained from most patients (N = 423 (63%)) displayed at least 1 alteration...
August 14, 2017: Cancer Research
https://www.readbyqxmd.com/read/28807054/transcriptomic-profile-of-tobacco-in-response-to-tomato-zonate-spot-orthotospovirus-infection
#9
Changjun Huang, Yupeng Cun, Haiqin Yu, Zhijun Tong, Bingguang Xiao, Zhongbang Song, Bingwu Wang, Yongping Li, Yong Liu
BACKGROUND: Tomato zonate spot virus (TZSV), a dominant species of thrips-transmitted orthotospoviruses in Yunnan and Guangxi provinces in China, causes significant loss of yield in lots of crops and is a major threat to incomes of rural families. However, the detailed molecular mechanism of crop disease caused by TZSV remains obscure. METHODS: Next-generation sequencing (NGS)-based transcriptome analysis (RNA-seq) was performed to investigate and compare the gene expression changes in systemic leaves of tobacco upon infection with TZSV and mock-inoculated plants as a control...
August 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/28805986/histiocytic-sarcoma-new-insights-into-fna-cytomorphology-and-molecular-characteristics
#10
Yin P Hung, Scott B Lovitch, Xiaohua Qian
BACKGROUND: Histiocytic sarcoma (HS) is a rare malignant neoplasm showing morphologic and immunophenotypic features of histiocytes. Molecular characteristics of HS and fine-needle aspiration (FNA) criteria for its diagnosis have not been established. METHODS: A case series of HS in 8 FNA samples from 6 patients was reviewed along with histopathologic and clinical data. Immunohistochemistry was performed on cell blocks (3 cases), core biopsies (5 cases), and surgical specimens (4 cases)...
August 2017: Cancer
https://www.readbyqxmd.com/read/28805163/cryptosporidium-in-fish-alternative-sequencing-approaches-and-analyses-at-multiple-loci-to-resolve-mixed-infections
#11
Andrea Paparini, Rongchang Yang, Linda Chen, Kaising Tong, Susan Gibson-Kueh, Alan Lymbery, Una M Ryan
Currently, the systematics, biology and epidemiology of piscine Cryptosporidium species are poorly understood. Here, we compared Sanger ‒ and next-generation ‒ sequencing (NGS), of piscine Cryptosporidium, at the 18S rRNA and actin genes. The hosts comprised 11 ornamental fish species, spanning four orders and eight families. The objectives were: to (i) confirm the rich genetic diversity of the parasite and the high frequency of mixed infections; and (ii) explore the potential of NGS in the presence of complex genetic mixtures...
August 14, 2017: Parasitology
https://www.readbyqxmd.com/read/28803971/otp-an-automatized-system-for-managing-and-processing-ngs-data
#12
Eva Reisinger, Lena Genthner, Jules Kerssemakers, Philip Kensche, Stefan Borufka, Alke Jugold, Andreas Kling, Manuel Prinz, Ingrid Scholz, Gideon Zipprich, Roland Eils, Christian Lawerenz, Jürgen Eils
The One Touch Pipeline (OTP) is an automation platform managing Next-Generation Sequencing (NGS) data and calling bioinformatic pipelines for processing these data. OTP handles the complete digital process from import of raw sequence data via alignment of sequencing reads to identify genomic events in an automated and scalable way. Three major goals are pursued: firstly, reduction of human resources required for data management by introducing automated processes. Secondly, reduction of time until the sequences can be analyzed by bioinformatic experts, by executing all operations more reliably and quickly...
August 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28803919/therapy-related-clonal-hematopoiesis-in-patients-with-non-hematologic-cancers-is-common-and-associated-with-adverse-clinical-outcomes
#13
Catherine C Coombs, Ahmet Zehir, Sean M Devlin, Ashwin Kishtagari, Aijazuddin Syed, Philip Jonsson, David M Hyman, David B Solit, Mark E Robson, José Baselga, Maria E Arcila, Marc Ladanyi, Martin S Tallman, Ross L Levine, Michael F Berger
Clonal hematopoiesis (CH), as evidenced by recurrent somatic mutations in leukemia-associated genes, commonly occurs among aging human hematopoietic stem cells. We analyzed deep-coverage, targeted, next-generation sequencing (NGS) data of paired tumor and blood samples from 8,810 individuals to assess the frequency and clinical relevance of CH in patients with non-hematologic malignancies. We identified CH in 25% of cancer patients, with 4.5% harboring presumptive leukemia driver mutations (CH-PD). CH was associated with increased age, prior radiation therapy, and tobacco use...
August 9, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28803747/novel-heterozygous-mutations-of-the-insr-gene-in-a-familial-case-of-donohue-syndrome
#14
Litao Qin, Xiaobo Li, Qiaofang Hou, Hongdan Wang, Guiyu Lou, Tao Li, Li Wang, Hongyan Liu, Xichuan Li, Shixiu Liao
Donohue syndrome (DS), a rare autosomal recessive disease which represents severe insulin resistance, pre- and postnatal growth retardation, hypertrichosis, and dysmorphic features, is caused by mutations in the insulin receptor (INSR) gene. Here, we have reported the clinical, molecular, and biochemical characterizations of a patient with DS. In this article, we have also reported a case with 2 novel INSR mutations and the DS phenotype. Using next-generation sequencing (NGS), we screened 27 known genes involved in inherited maturity-onset diabetes of the young (MODY) and identified compound heterozygous mutations in the INSR gene in the patient with DS, c...
August 10, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28802713/detecting-exact-breakpoints-of-deletions-with-diversity-in-hepatitis-b-viral-genomic-dna-from-next-generation-sequencing-data
#15
Ji-Hong Cheng, Wen-Chun Liu, Ting-Tsung Chang, Sun-Yuan Hsieh, Vincent S Tseng
Many studies have suggested that deletions of Hepatitis B Viral (HBV) are associated with the development of progressive liver diseases, even ultimately resulting in hepatocellular carcinoma (HCC). Among the methods for detecting deletions from next-generation sequencing (NGS) data, few methods considered the characteristics of virus, such as high evolution rates and high divergence among the different HBV genomes. Sequencing high divergence HBV genome sequences using the NGS technology outputs millions of reads...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28799806/elevated-serum-level-of-ca125-is-a-biomarker-that-can-be-used-to-alter-prognosis-determined-by-brca-mutation-and-family-history-in-ovarian-cancer
#16
Weiling Liu, Zhizhong Wang, Jie Ma, Yangyang Hou, Jiuzhou Zhao, Bing Dong, Shichun Tu, Li Wang, Yongjun Guo
AIMS: In this study, we determined whether serum tumor markers (STMs), including CA125, are associated with BRCA mutation status and if they can be used prognostically in sporadic ovarian cancer (SOC) and familial ovarian cancer (FOC). METHODS: BRCA gene mutations were screened using next-generation sequencing (NGS) in 31 FOC and 66 SOC patients enrolled between 2013 and 2014. The serum levels of STM CEA, CA125, CA199, and HE4 were also measured in these patients to determine the prognostic potential of these markers and their association with BRCA mutations...
August 11, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28799325/comparison-between-next-generation-and-sanger-based-sequencing-for-the-detection-of-transmitted-drug-resistance-mutations-among-recently-infected-hiv-1-patients-in-israel-2000-2014
#17
Roy Moscona, Daniela Ram, Marina Wax, Efrat Bucris, Itzchak Levy, Ella Mendelson, Orna Mor
INTRODUCTION: Transmitted drug-resistance mutations (TDRM) may hamper successful anti-HIV-1 therapy and impact future control of the HIV-1 epidemic. Recently infected, therapy-naïve individuals are best suited for surveillance of such TDRM. In this study, TDRM, detected by next-generation sequencing (NGS) were compared to those identified by Sanger-based population sequencing (SBS) in recently infected HIV-1 patients. METHODS: Historical samples from 80 recently infected HIV-1 patients, diagnosed between 2000 and 2014, were analysed by MiSeq (NGS) and ABI (SBS)...
August 11, 2017: Journal of the International AIDS Society
https://www.readbyqxmd.com/read/28798766/toward-genomics-based-breeding-in-c3-cool-season-perennial-grasses
#18
REVIEW
Shyamal K Talukder, Malay C Saha
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28797221/use-of-genotyping-by-sequencing-to-determine-the-genetic-structure-in-the-medicinal-plant-chamomile-and-to-identify-flowering-time-and-alpha-bisabolol-associated-snp-loci-by-genome-wide-association-mapping
#19
Lars-Gernot Otto, Prodyut Mondal, Jonathan Brassac, Susanne Preiss, Jörg Degenhardt, Sang He, Jochen Christoph Reif, Timothy Francis Sharbel
BACKGROUND: Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28796570/pedigree-analysis-of-familial-primary-concomitant-horizontal-strabismus-in-northern-india
#20
Zia Chaudhuri, Jibin John, Satinder Aneja, B K Thelma
PURPOSE: Familial clustering of common forms of primary strabismus like esotropia (ET) and exotropia (XT) is observed in a proportion of the strabismus cohort. The genetic components of this remain unidentified. Linkage studies have demonstrated susceptibility locus for primary strabismus at the STBMS1 locus on 7p22.1 as well as other loci on 4q28.3 and 7q31.2. Recently next generation sequencing (NGS) technology has emerged as a powerful tool in discovery genomics and a large number of novel disease-causing variants are being reported...
August 10, 2017: Strabismus
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