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https://www.readbyqxmd.com/read/28346895/wheat-genomics-comes-of-age
#1
REVIEW
Cristobal Uauy
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs...
March 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28346704/the-chloroplast-rna-helicase-ise2-is-required-for-multiple-chloroplast-rna-processing-steps-in-arabidopsis-thaliana
#2
Krzysztof Bobik, Tyra N McCray, Ben Ernest, Jessica C Fernandez, Katharine A Howell, Thomas Lane, Margaret Staton, Tessa M Burch-Smith
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346340/a-place-to-call-home-an-analysis-of-the-bacterial-communities-in-two-tethya-rubra-samaai-and-gibbons-2005-populations-in-algoa-bay-south-africa
#3
Samantha C Waterworth, Meesbah Jiwaji, Jarmo-Charles J Kalinski, Shirley Parker-Nance, Rosemary A Dorrington
Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding...
March 25, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28346228/somatic-mutations-and-progressive-monosomy-modify-samd9-related-phenotypes-in-humans
#4
Federica Buonocore, Peter Kühnen, Jenifer P Suntharalingham, Ignacio Del Valle, Martin Digweed, Harald Stachelscheid, Noushafarin Khajavi, Mohammed Didi, Angela F Brady, Oliver Blankenstein, Annie M Procter, Paul Dimitri, Jerry K H Wales, Paolo Ghirri, Dieter Knöbl, Brigitte Strahm, Miriam Erlacher, Marcin W Wlodarski, Wei Chen, George K Kokai, Glenn Anderson, Deborah Morrogh, Dale A Moulding, Shane A McKee, Charlotte M Niemeyer, Annette Grüters, John C Achermann
It is well established that somatic genomic changes can influence phenotypes in cancer, but the role of adaptive changes in developmental disorders is less well understood. Here we have used next-generation sequencing approaches to identify de novo heterozygous mutations in sterile α motif domain-containing protein 9 (SAMD9, located on chromosome 7q21.2) in 8 children with a multisystem disorder termed MIRAGE syndrome that is characterized by intrauterine growth restriction (IUGR) with gonadal, adrenal, and bone marrow failure, predisposition to infections, and high mortality...
March 27, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28345786/a-de-novo-nonsense-mutation-in-zbtb18-plus-a-de-novo-15q13-3-microdeletion-in-a-6-year-old-female
#5
Nadja Ehmke, Sylvio Karge, Johannes Buchmann, Dirk Korinth, Denise Horn, Olaf Reis, Frank Häßler
ZBTB18 has been proposed as candidate gene for microcephaly and abnormalities of the corpus callosum based on overlapping microdeletions of 1q43q44. More recently, de novo mutations of ZBTB18 have been identified in patients with syndromic and non-syndromic intellectual disability. Heterozygous microdeletions of 15q13.3 encompassing the candidate gene CHRNA7 are associated with developmental delay or intellectual disability with speech problems, hypotonia, and seizures. They are characterized by significant variability and reduced penetrance...
March 27, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28345074/single-cell-rna-seq-and-computational-analysis-using-temporal-mixture-modelling-resolves-th1-tfh-fate-bifurcation-in-malaria
#6
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto, Michael J T Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T Bunn, Christian R Engwerda, William R Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Differentiation of naïve CD4(+) T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice...
March 3, 2017: Science Immunology
https://www.readbyqxmd.com/read/28344976/a-metataxonomic-approach-could-be-considered-for-cattle-clinical-mastitis-diagnostics
#7
Joanne W H Oultram, Erika K Ganda, Sarah C Boulding, Rodrigo C Bicalho, Georgios Oikonomou
Mastitis is one of the most costly diseases affecting the dairy industry, and identification of the causative microorganism(s) is essential. Here, we report the use of next-generation sequencing of bacterial 16S rRNA genes for clinical mastitis diagnosis. We used 65 paired milk samples, collected from the mastitic and a contralateral healthy quarter of mastitic dairy cattle to evaluate the technique as a potential alternative to bacterial culture or targeted PCR. One large commercial dairy farm was used, with one trained veterinarian collecting the milk samples...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28344162/identification-of-genetic-markers-of-resistance-to-echinocandins-azoles-and-5-fluorocytosine-in-candida-glabrata-by-next-generation-sequencing-a-feasibility-study
#8
Chayanika Biswas, Sharon C-A Chen, Catriona Halliday, Karina Kennedy, E Geoffrey Playford, Deborah J Marriott, Monica A Slavin, Tania C Sorrell, Vitali Sintchenko
OBJECTIVES: Multi-antifungal drug resistance in Candida glabrata is increasing. We examined the feasibility of next generation sequencing (NGS) to investigate the presence of antifungal drug resistance markers in C. glabrata. METHODS: The antifungal susceptibility of 12 clinical isolates and one ATCC strain of C. glabrata was determined using the Sensititre YeastOne® YO10 assay. These included three isolate pairs where the second isolate of each pair had developed a rise in drug MICs...
March 23, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28342698/targeted-exome-sequencing-and-chromosomal-microarray-for-the-molecular-diagnosis-of-nevoid-basal-cell-carcinoma-syndrome
#9
Yoshihiro Matsudate, Takuya Naruto, Yumiko Hayashi, Mitsuyoshi Minami, Mikiko Tohyama, Kenji Yokota, Daisuke Yamada, Issei Imoto, Yoshiaki Kubo
BACKGROUND: Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder mainly caused by heterozygous mutations of PTCH1. In addition to characteristic clinical features, detection of a mutation in causative genes is reliable for the diagnosis of NBCCS; however, no mutations have been identified in some patients using conventional methods. OBJECTIVE: To improve the method for the molecular diagnosis of NBCCS. METHODS: We performed targeted exome sequencing (TES) analysis using a multi-gene panel, including PTCH1, PTCH2, SUFU, and other sonic hedgehog signaling pathway-related genes, based on next-generation sequencing (NGS) technology in 8 cases in whom possible causative mutations were not detected by previously performed conventional analysis and 2 recent cases of NBCCS...
March 11, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28341590/guidelines-for-validation-of-next-generation-sequencing-based-oncology-panels-a-joint-consensus-recommendation-of-the-association-for-molecular-pathology-and-college-of-american-pathologists
#10
REVIEW
Lawrence J Jennings, Maria E Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M Lubin, John Pfeifer, Robyn L Temple-Smolkin, Karl V Voelkerding, Marina N Nikiforova
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341588/targeted-next-generation-sequencing-of-51-genes-involved-in-primary-electrical-disease
#11
Dorien Proost, Johan Saenen, Geert Vandeweyer, Annelies Rotthier, Maaike Alaerts, Emeline M Van Craenenbroeck, Joachim Van Crombruggen, Geert Mortier, Wim Wuyts, Christiaan Vrints, Jurgen Del Favero, Bart Loeys, Lut Van Laer
Primary electrical disease (PED) is characterized by cardiac arrhythmias, which can lead to sudden cardiac death in the absence of detectable structural heart disease. PED encompasses a diversity of inherited syndromes, predominantly Brugada syndrome, early repolarization syndrome, long QT syndrome, short QT syndrome, arrhythmogenic right ventricular cardiomyopathy, and catecholaminergic polymorphic ventricular tachycardia. To overcome the diagnostic challenges imposed by the clinical and genetic heterogeneity of PED, we developed a targeted gene panel for next-generation sequencing of 51 PED genes...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341207/transcriptome-analysis-of-airborne-pm2-5-induced-detrimental-effects-on-human-keratinocytes
#12
Hyoung-June Kim, Il-Hong Bae, Eui Dong Son, Juyearl Park, Nari Cha, Hyewon Na, Changjo Jung, You-Seak Go, Dae-Yong Kim, Tae Ryong Lee, Dong Wook Shin
Ambient air pollution is becoming more severe worldwide, posing a serious threat to human health. Fine airborne particles of particulate matter (PM2.5) show higher cytotoxicity than other coarse fractions. Indeed, PM2.5 induces cardiovascular or respiratory damage; however, few studies have evaluated the detrimental effect of PM2.5 to normal human skin. We used a next-generation sequencing-based (RNA-Seq) method with transcriptome and Gene Ontology (GO) enrichment analysis to determine the harmful influences of PM2...
March 21, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28340953/clinical-features-of-chinese-patients-with-gerstmann-str%C3%A3-ussler-scheinker-identified-by-targeted-next-generation-sequencing
#13
Hong-Fu Li, Zhi-Jun Liu, Hai-Lin Dong, Juan-Juan Xie, Shao-Yun Zhao, Wang Ni, Yi Dong, Zhi-Ying Wu
Gerstmann-Sträussler-Scheinker (GSS) is an autosomal dominant neurodegenerative disease due to mutations within prion protein (PRNP) gene. Clinically, it is not easy to distinguish GSS from spinocerebellar ataxia (SCA), especially in the early stage of disease. We aimed to identify genetic mutations in 8 Chinese pedigrees with dominant ataxia but excluded dynamic mutations of SCA genes. Targeted next-generation sequencing was performed in the 8 probands. A customized panel was designed to capture 24 known causative genes, including 15 autosomal dominant SCA genes and 9 dementia-related genes...
January 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28340560/a-novel-pore-region-mutation-c-887g%C3%A2-%C3%A2-a-p-g296d-in-kcnq4-causing-hearing-loss-in-a-chinese-family-with-autosomal-dominant-non-syndromic-deafness-2
#14
Bangqing Huang, Yanping Liu, Xue Gao, Jincao Xu, Pu Dai, Qingwen Zhu, Yongyi Yuan
BACKGROUND: Hereditary non-syndromic hearing loss is the most common inherited sensory defect in humans. The KCNQ4 channel belongs to a family of potassium ion channels that play crucial roles in physiology and disease. Mutations in KCNQ4 underlie deafness non-syndromic autosomal dominant 2, a subtype of autosomal dominant, progressive, high-frequency hearing loss. METHODS: A six-generation Chinese family from Hebei Province with autosomal dominantly inherited, sensorineural, postlingual, progressive hearing loss was enrolled in this study...
March 24, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28340459/transcriptional-profiling-of-porcine-granulosa-cells-exposed-to-2-3-7-8-tetrachlorodibenzo-p-dioxin
#15
Agnieszka Sadowska, Anna Nynca, Monika Ruszkowska, Lukasz Paukszto, Kamil Myszczynski, Karina Orlowska, Sylwia Swigonska, Tomasz Molcan, Jan P Jastrzebski, Renata E Ciereszko
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating the environment. An exposure of living organisms to TCDD may result in numerous disorders, including reproductive pathologies. The aim of the current study was to examine the effects of TCDD on the transcriptome of porcine granulosa cell line AVG-16. By employing next-generation sequencing (NGS) we aimed to identify genes potentially involved in the mechanism of TCDD action and toxicity in porcine granulosa cells...
March 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28339163/next-generation-sequencing-of-urine-specimens-a-novel-platform-for-genomic-analysis-in-patients-with-non-muscle-invasive-urothelial-carcinoma-treated-with-bacille-calmette-gu%C3%A3-rin
#16
Sasinya N Scott, Irina Ostrovnaya, Caroline M Lin, Nancy Bouvier, Bernard H Bochner, Gopakumar Iyer, David Solit, Michael F Berger, Oscar Lin
BACKGROUND: Biopsies from patients with high-risk (HR) non-muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guérin (BCG) treatment...
March 24, 2017: Cancer
https://www.readbyqxmd.com/read/28338930/expath-tool-a-system-for-comprehensively-analyzing-regulatory-pathways-and-coexpression-networks-from-high-throughput-transcriptome-data
#17
Han-Qin Zheng, Nai-Yun Wu, Chi-Nga Chow, Kuan-Chieh Tseng, Chia-Hung Chien, Yu-Cheng Hung, Guan-Zhen Li, Wen-Chi Chang
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data...
March 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338918/integrated-mirna-and-mrna-expression-profiling-reveals-the-response-regulators-of-a-susceptible-tomato-cultivar-to-early-blight-disease
#18
Deepti Sarkar, Ranjan Kumar Maji, Sayani Dey, Arijita Sarkar, Zhumur Ghosh, Pallob Kundu
Early blight, caused by the fungus Alternaria solani, is a devastating foliar disease of tomatoes, causes massive yield loss each year worldwide. Molecular basis of the compatible host-pathogen interaction was elusive. We adopted next generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed during Alternaria-stress in tomato. Some of the interesting findings were also validated by alternative techniques. Our analysis revealed 181 known-miRNAs, belonging to 121 miRNA families, of which 67 miRNAs showed at least 2-fold change in expression level with the majority being downregulated...
March 3, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338218/evaluation-of-targeted-exome-sequencing-for-28-protein-based-blood-group-systems-including-the-homologous-gene-systems-for-blood-group-genotyping
#19
Elizna M Schoeman, Genghis H Lopez, Eunike C McGowan, Glenda M Millard, Helen O'Brien, Eileen V Roulis, Yew-Wah Liew, Jacqueline R Martin, Kelli A McGrath, Tanya Powley, Robert L Flower, Catherine A Hyland
BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform...
March 24, 2017: Transfusion
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#20
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
March 21, 2017: Journal of Biomolecular Techniques: JBT
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