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https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#1
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28224495/hidden-markov-models-in-bioinformatics-snv-inference-from-next-generation-sequence
#2
Jiawen Bian, Xiaobo Zhou
The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224058/characterization-of-microsatellite-markers-in-two-exploited-african-trees-entandrophragma-candollei-and-e-utile-meliaceae
#3
Franck S Monthe, Jérôme Duminil, Félicien Tosso, Jérémy Migliore, Olivier J Hardy
PREMISE OF THE STUDY: Multiplexes of nuclear microsatellite primers were developed to investigate population genetic structure and diversity in two exploited African rainforest trees: Entandrophragma candollei and E. utile (Meliaceae). METHODS AND RESULTS: Microsatellite isolation was performed simultaneously on two nonenriched genomic libraries after next-generation sequencing. We developed 16 and 22 polymorphic markers for E. candollei and E. utile in three and four multiplexes, respectively...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224057/identification-and-characterization-of-microsatellite-markers-in-pinus-kesiya-var-langbianensis-pinaceae
#4
Nian-Hui Cai, Yu-Lan Xu, Da-Wei Wang, Shi Chen, Gen-Qian Li
PREMISE OF THE STUDY: Microsatellite primers were developed in Pinus kesiya var. langbianensis (Pinaceae), a species native to southwestern China, to investigate its genetic diversity and population structure in order to provide information for the conservation and management of this species. METHODS AND RESULTS: Using next-generation sequencing, a total of 2349 putative simple sequence repeat primer pairs were designed. Eighteen polymorphic markers in 60 individuals belonging to four populations of P...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28223993/diacylglycerol-kinases-are-widespread-in-higher-plants-and-display-inducible-gene-expression-in-response-to-beneficial-elements-metal-and-metalloid-ions
#5
Hugo F Escobar-Sepúlveda, Libia I Trejo-Téllez, Paulino Pérez-Rodríguez, Juan V Hidalgo-Contreras, Fernando C Gómez-Merino
Diacylglycerol kinases (DGKs) are pivotal signaling enzymes that phosphorylate diacylglycerol (DAG) to yield phosphatidic acid (PA). The biosynthesis of PA from phospholipase D (PLD) and the coupled phospholipase C (PLC)/DGK route is a crucial signaling process in eukaryotic cells. Next to PLD, the PLC/DGK pathway is the second most important generator of PA in response to biotic and abiotic stresses. In eukaryotic cells, DGK, DAG, and PA are implicated in vital processes such as growth, development, and responses to environmental cues...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223979/broadcast-spawning-coral-mussismilia-hispida-can-vertically-transfer-its-associated-bacterial-core
#6
Deborah C A Leite, Pedro Leão, Amana G Garrido, Ulysses Lins, Henrique F Santos, Débora O Pires, Clovis B Castro, Jan D van Elsas, Carla Zilberberg, Alexandre S Rosado, Raquel S Peixoto
The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#7
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223367/coordination-of-myeloid-differentiation-with-reduced-cell-cycle-progression-by-pu-1-induction-of-micrornas-targeting-cell-cycle-regulators-and-lipid-anabolism
#8
Lauren A Solomon, Shreya Podder, Jessica He, Nicholas L Jackson Chornenki, Kristen Gibson, Rachel G Ziliotto, Jess Rhee, Rodney P DeKoter
During macrophage development, myeloid progenitor cells undergo terminal differentiation coordinated with reduced cell cycle progression. Differentiation of macrophages from myeloid progenitors is accompanied by increased expression of the E26-transformation specific transcription factor PU.1. Reduced PU.1 expression leads to increased proliferation and impaired differentiation of myeloid progenitor cells. It is not understood how PU.1 coordinates macrophage differentiation with reduced cell cycle progression...
February 21, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28223188/next-generation-sequencing-unravels-homozygous-mutation-in-glucose-6-phosphate-isomerase-gpic-1040g-a-p-arg347his-causing-hemolysis-in-an-indian-infant
#9
Manu Jamwal, Anu Aggarwal, Anirban Das, Arindam Maitra, Prashant Sharma, Shekhar Krishnan, Neeraj Arora, Deepak Bansal, Reena Das
INTRODUCTION: Inherited anemias diagnostic workup requires a step-wise algorithm. Causal genes implicated in congenital hemolytic anemia are numerous, making a gene-by-gene approach by Sanger sequencing time consuming, expensive and labour intensive. Targeted resequencing can be of great use in explaining these cases. METHODOLOGY: Six months female presented with neonatal jaundice and negative family history. Clinical and laboratory evidences were suggestive of hemolytic anemia...
February 18, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28222683/manananggal-a-novel-viewer-for-alternative-splicing-events
#10
Matthias Barann, Ralf Zimmer, Fabian Birzele
BACKGROUND: Alternative splicing is an important cellular mechanism that can be analyzed by RNA sequencing. However, identification of splicing events in an automated fashion is error-prone. Thus, further validation is required to select reliable instances of alternative splicing events (ASEs). There are only few tools specifically designed for interactive inspection of ASEs and available visualization approaches can be significantly improved. RESULTS: Here, we present Manananggal, an application specifically designed for the identification of splicing events in next generation sequencing data...
February 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28222664/prevalence-and-coexistence-of-kras-braf-pik3ca-nras-tp53-and-apc-mutations-in-indian-colorectal-cancer-patients-next-generation-sequencing-based-cohort-study
#11
Mayank Jauhri, Akanksha Bhatnagar, Satish Gupta, Manasa Bp, Sachin Minhas, Yogender Shokeen, Shyam Aggarwal
Colorectal cancer incidences are on a rise in India. In this study, we have analyzed the mutation frequencies of six potential biomarkers, their coexistence, association with clinicopathological characteristics, and tumor location in Indian colorectal cancer patients. Next-generation sequencing was performed to identify mutations in the six potential biomarker genes using formalin-fixed paraffin-embedded tissue blocks of 112 colorectal cancer patients. The mutation frequency observed in KRAS, BRAF, PIK3CA, NRAS, TP53, and APC was 35...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28222336/a-two-step-approach-for-sequencing-spliceosome-related-genes-as-a-complementary-diagnostic-assay-in-mds-patients-with-ringed-sideroblasts
#12
Kamila Janusz, Mónica Del Rey, María Abáigar, Rosa Collado, David Ivars, María Hernández-Sánchez, Alberto Valiente, Cristina Robledo, Rocío Benito, María Díez-Campelo, Fernando Ramos, Alexander Kohlmann, Consuelo Del Cañizo, Jesús María Hernández-Rivas
Our study aimed to analyze the presence of mutations in SF3B1 and other spliceosome-related genes in myelodysplastic syndromes with ringed sideroblasts (MDS-RS) by combining conventional Sanger and next-generation sequencing (NGS) methods, and to determine the feasibility of this approach in a clinical setting. 122 bone marrow samples from MDS-RS patients were studied. Initially, exons 14 and 15 of the SF3B1 gene were analyzed by Sanger sequencing. Secondly, they were studied by NGS covering besides SF3B1, SRSF2, U2AF1 and ZRSR2 genes...
February 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28222323/a-case-report-of-the-clear-cell-variant-of-gallbladder-carcinoma
#13
Ravi Maharaj, Christo Cave, Kevin Sarran, Nigel Bascombe, Dilip Dan, Wesley Greaves, Wayne A Warner
INTRODUCTION: Clear cell gallbladder carcinoma accounts for less than 1% of all gallbladder malignancies and demonstrates its unique histopathological characteristics in patients with no prior medical illness or familial predisposition. PRESENTATION OF CASE: Here we present a case of a 56-year-old female, with no prior medical conditions presented with a 2-month history of upper abdominal pain. Routine hematological and biochemical tests were unremarkable. An abdominal ultrasound revealed the presence of a gallbladder calculi, and a fundic mass while magnetic resonance cholangiopancreatography revealed a 8...
January 12, 2017: International Journal of Surgery Case Reports
https://www.readbyqxmd.com/read/28222155/glm-based-optimization-of-ngs-data-analysis-a-case-study-of-roche-454-ion-torrent-pgm-and-illumina-nextseq-sequencing-data
#14
Sarah Sandmann, Aniek O de Graaf, Bert A van der Reijden, Joop H Jansen, Martin Dugas
BACKGROUND: There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms. METHODS: We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines...
2017: PloS One
https://www.readbyqxmd.com/read/28222152/alteration-of-the-exdna-profile-in-blood-serum-of-llc-bearing-mice-under-the-decrease-of-tumour-invasion-potential-by-bovine-pancreatic-dnase-i-treatment
#15
Ludmila A Alekseeva, Nadezhda L Mironova, Evgenyi V Brenner, Alexander M Kurilshikov, Olga A Patutina, Marina A Zenkova
Taking into account recently obtained data indicating the participation of circulating extracellular DNA (exDNA) in tumorigenesis, enzymes with deoxyribonucleic activity have again been considered as potential antitumour and antimetastatic drugs. Previously, using murine Lewis lung carcinoma and hepatocellular carcinoma A1 tumour models, we have shown the antimetastatic activity of bovine DNase I, which correlates with an increase of DNase activity and a decrease of exDNA concentration in the blood serum of tumour-bearing mice...
2017: PloS One
https://www.readbyqxmd.com/read/28220395/single-cell-sequencing-a-distinct-new-field
#16
REVIEW
Jian Wang, Yuanlin Song
Single cell sequencing (SCS) has become a new approach to study biological heterogeneity. The advancement in technologies for single cell isolation, amplification of genome/transcriptome and next-generation sequencing enables SCS to reveal the inherent properties of a single cell from the large scale of the genome, transcriptome or epigenome at high resolution. Recently, SCS has been widely applied in various clinical and research fields, such as cancer biology and oncology, immunology, microbiology, neurobiology and prenatal diagnosis...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28220254/hiv-1-persistent-viremia-is-frequently-followed-by-episodes-of-low-level-viremia
#17
Marek Widera, Miriam Dirks, Barbara Bleekmann, Robert Jablonka, Martin Däumer, Hauke Walter, Robert Ehret, Jens Verheyen, Stefan Esser
After the start of antiretroviral therapy (ART), plasma HIV-RNA levels should fall below the limit of detection (LOD) within 24 weeks. Hence, the prolonged decline of HIV-RNA after ART initiation is defined as persistent viremia (PV). In this retrospective study, we analyzed factors associated with PV. Next-generation sequencing of viral RNA/DNA was performed to study viral evolution and the emergence of drug-resistance mutations in HIV-infected patients with PV (n = 20). In addition, HIV-DNA species, immunological parameters, and clinical data of the patients were analyzed...
February 20, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/28220139/genome-wide-single-nucleotide-polymorphism-discovery-and-the-construction-of-a-high-density-genetic-map-for-melon-cucumis-melo-l-using-genotyping-by-sequencing
#18
Che-Wei Chang, Yu-Hua Wang, Chih-Wei Tung
Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220132/identification-of-marker-trait-associations-for-lint-traits-in-cotton
#19
Muhammad A Iqbal, Mehboob-Ur- Rahman
Harvesting high quality lint, a long-awaited breeding goal-accomplished partly, can be achieved by identifying DNA markers which could be used for diagnosing cotton plants containing the desired traits. In the present studies, a total of 185 cotton genotypes exhibiting diversity for lint traits were selected from a set of 546 genotypes evaluated for fiber traits in 2009. These genotypes were extensively studied for three consecutive years (2011-2013) at three different locations. Significant genetic variations were found for average boll weight, ginning out turn (GOT), micronaire value, staple length, fiber bundle strength, and uniformity index...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220018/germline-variants-in-familial-pituitary-tumour-syndrome-genes-are-common-in-young-patients-and-families-with-additional-endocrine-tumours
#20
Sunita Mc De Sousa, Mark J McCabe, Kathy Wu, Tony Roscioli, Velimir Gayevskiy, Katelyn Brook, Lesley Rawlings, Hamish S Scott, Tanya J Thompson, Peter Earls, Anthony J Gill, Mark J Cowley, Marcel E Dinger, Ann I McCormack
Objective: Familial pituitary tumour syndromes (FPTS) account for 5% of pituitary adenomas. Multi-gene analysis via next generation sequencing (NGS) may unveil greater prevalence and inform clinical care. We aimed to identify germline variants in selected patients with pituitary adenomas using a targeted NGS panel. Design: We undertook a nation-wide cross-sectional study of patients with pituitary adenomas with onset ≤40 years of age and/or other personal/family history of endocrine neoplasia. A custom NGS panel was performed on germline DNA to interrogate eight FPTS genes...
February 20, 2017: European Journal of Endocrinology
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