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https://www.readbyqxmd.com/read/28103613/tissue-based-next-generation-sequencing-application-in-a-universal-healthcare-system
#1
REVIEW
Seán O Hynes, Brendan Pang, Jacqueline A James, Perry Maxwell, Manuel Salto-Tellez
In the context of solid tumours, the evolution of cancer therapies to more targeted and nuanced approaches has led to the impetus for personalised medicine. The targets for these therapies are largely based on the driving genetic mutations of the tumours. To track these multiple driving mutations the use of next generation sequencing (NGS) coupled with a morphomolecular approach to tumours, has the potential to deliver on the promises of personalised medicine. A review of NGS and its application in a universal healthcare (UHC) setting is undertaken as the technology has a wide appeal and utility in diagnostic, clinical trial and research paradigms...
January 19, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28103008/quantitative-tracking-of-combinatorially-engineered-populations-with-multiplexed-binary-assemblies
#2
Ramsey Zeitoun, Gur Pines, William C Grau, Ryan T Gill
Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory timescales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28102863/a-taxonomy-of-medical-uncertainties-in-clinical-genome-sequencing
#3
Paul K J Han, Kendall L Umstead, Barbara A Bernhardt, Robert C Green, Steven Joffe, Barbara Koenig, Ian Krantz, Leo B Waterston, Leslie G Biesecker, Barbara B Biesecker
PURPOSE: Clinical next-generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of an unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. METHODS: Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts and themes were extracted in order to expand on a previously published three-dimensional taxonomy of medical uncertainty...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102861/clinical-utility-of-next-generation-sequencing-for-inherited-bone-marrow-failure-syndromes
#4
Hideki Muramatsu, Yusuke Okuno, Kenichi Yoshida, Yuichi Shiraishi, Sayoko Doisaki, Atsushi Narita, Hirotoshi Sakaguchi, Nozomu Kawashima, Xinan Wang, Yinyan Xu, Kenichi Chiba, Hiroko Tanaka, Asahito Hama, Masashi Sanada, Yoshiyuki Takahashi, Hitoshi Kanno, Hiroki Yamaguchi, Shouichi Ohga, Atsushi Manabe, Hideo Harigae, Shinji Kunishima, Eiichi Ishii, Masao Kobayashi, Kenichi Koike, Kenichiro Watanabe, Etsuro Ito, Minoru Takata, Miharu Yabe, Seishi Ogawa, Satoru Miyano, Seiji Kojima
PURPOSE: Precise genetic diagnosis of inherited bone marrow failure syndromes (IBMFS), a heterogeneous group of genetic disorders, is challenging but essential for precise clinical decision making. METHODS: We analyzed 121 IBMFS patients using a targeted sequencing covering 184 associated genes and 250 IBMFS patients using whole-exome sequencing (WES). RESULTS: We achieved successful genetic diagnoses for 53 of 121 patients (44%) using targeted sequencing and for 68 of 250 patients (27%) using WES...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102674/2d-ir-spectroscopy-shows-that-optimised-dna-minor-groove-binding-of-hoechst33258-follows-an-induced-fit-model
#5
Lennart A I Ramakers, Gordon Hithell, John J May, Gregory M Greetham, Paul M Donaldson, Michael Towrie, Anthony W Parker, Glenn A Burley, Neil T Hunt
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region...
January 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28102232/aetiology-and-management-of-hereditary-aortopathy
#6
REVIEW
Aline Verstraeten, Ilse Luyckx, Bart Loeys
Aortic aneurysms are a major health problem because they account for 1-2% of all deaths in the Western population. Although abdominal aortic aneurysms (AAAs) are more prevalent than thoracic aortic aneurysms (TAAs), TAAs have been more exhaustively studied over the past 2 decades because they have a higher heritability and affect younger individuals. Gene identification in both syndromic and nonsyndromic TAA is proceeding at a rapid pace and has already pinpointed >20 genes associated with familial TAA risk...
January 19, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28102197/a-novel-dominant-gjb2-dfna3-mutation-in-a-chinese-family
#7
Hongyang Wang, Kaiwen Wu, Lan Yu, Linyi Xie, Wenping Xiong, Dayong Wang, Jing Guan, Qiuju Wang
To decipher the phenotype and genotype of a Chinese family with autosomal dominant non-syndromic hearing loss (ADNSHL) and a novel dominant missense mutation in the GJB2 gene (DFNA3), mutation screening of GJB2 was performed on the propositus from a five-generation ADNSHL family through polymerase chain reaction amplification and Sanger sequencing. The candidate variation and the co-segregation of the phenotype were verified in all ascertained family members. Targeted genes capture and next-generation sequencing (NGS) were performed to explore additional genetic variations...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102036/combining-one-step-sanger-sequencing-with-phasing-probe-hybridization-for-hla-class-i-typing-yields-rapid-g-group-resolution-predicting-99-of-unique-full-length-protein-sequences
#8
Bin Tu, Carly Masaberg, Lihua Hou, Daniel Behm, Peter Brescia, Nuri Cha, Kanthi Kariyawasam, Jar How Lee, Thoa Nong, John Sells, Paul Tausch, Ruyan Yang, Jennifer Ng, Carolyn Katovich Hurley
BACKGROUND: Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype. MATERIALS AND METHODS: Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization. This workflow, together with optimization of analysis software, was tested and refined during the typing of over 42,000 volunteers for an unrelated hematopoietic progenitor cell donor registry...
February 2017: HLA
https://www.readbyqxmd.com/read/28101802/cold-pcr-technologies-in-the-area-of-personalized-medicine-methodology-and-applications
#9
REVIEW
Florence Mauger, Alexandre How-Kit, Jörg Tost
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation...
January 18, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28101439/development-of-highly-variable-microsatellite-markers-for-the-tetraploid-silene-stellata-caryophyllaceae
#10
Juannan Zhou, Michele R Dudash, Charles B Fenster, Elizabeth A Zimmer
PREMISE OF THE STUDY: We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. METHODS AND RESULTS: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats...
December 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28101437/characterization-of-16-microsatellite-markers-for-the-oreinotinus-clade-of-viburnum-adoxaceae
#11
Syndi Barish, Mónica Arakaki, Erika J Edwards, Michael J Donoghue, Wendy L Clement
PREMISE OF THE STUDY: Microsatellite loci were isolated from four species of Viburnum (Adoxaceae) to study population structure and assess species boundaries among morphologically similar South American Viburnum species of the Oreinotinus clade. METHODS AND RESULTS: Using a microsatellite-enriched library and mining next-generation sequence data, 16 microsatellites were developed. Each locus was tested on two populations of V. triphyllum and one population of V...
December 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28100912/cryptic-splice-activation-but-not-exon-skipping-is-observed-in-minigene-assays-of-dystrophin-c-9361-1g-a-mutation-identified-by-ngs
#12
Emma Tabe Eko Niba, Atsushi Nishida, Van Khanh Tran, Dung Chi Vu, Masaaki Matsumoto, Hiroyuki Awano, Tomoko Lee, Yasuhiro Takeshima, Hisahide Nishio, Masafumi Matsuo
Next-generation sequencing (NGS) discloses nucleotide changes in the genome. Mutations at splicing regulatory elements are expected to cause splicing errors, such as exon skipping, cryptic splice site activation, partial exon loss or intron retention. In dystrophinopathy patients, prediction of splicing outcomes is essential to determine the phenotype: either severe Duchenne or mild Becker muscular dystrophy, based on the reading frame rule. In a Vietnamese patient, NGS identified a c.9361+1G>A mutation in the dystrophin gene and an additional DNA variation of A>G at +117 bases in intron 64...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100593/clinical-implications-of-dnmt3a-mutations-in-a-southeast-asian-cohort-of-acute-myeloid-leukaemia-patients
#13
Marcus Tan, Isaac K S Ng, Zhaojin Chen, Kenneth Ban, Christopher Ng, Lily Chiu, Elaine Seah, Mingxuan Lin, Bee Choo Tai, Benedict Yan, Chin Hin Ng, Wee-Joo Chng
AIMS: In recent years, genomic technologies have enabled the identification of mutations in acute myeloid leukaemia (AML). DNMT3A is a recurrently mutated epigenetic modifier gene in AML. To date, the prognostic significance of DNMT3A mutations has not been studied in a Southeast Asian AML population. We sought to investigate the clinical implications of DNMT3A mutations in a Southeast Asian cohort of AML patients. METHODS: DNMT3A mutations were identified using a targeted next-generation sequencing panel in 157 AML patients...
January 18, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28100494/quantification-of-bk-virus-standards-by-quantitative-real-time-pcr-and-droplet-digital-pcr-is-confounded-by-multiple-virus-populations-in-the-who-bkv-international-standard
#14
Allen C Bateman, Alexander L Greninger, Ederlyn E Atienza, Ajit P Limaye, Keith R Jerome, Linda Cook
BACKGROUND: The WHO recently released a BK virus (BKV) international standard. This study evaluated the WHO international standard and commercially available BKV standards by quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). METHODS: WHO, Exact Diagnostics, Acrometrix, and Zeptometrix BKV standards were tested by qPCR and ddPCR. Two preparations of NIST BKV clones were also tested. Nucleic acid was extracted with the Roche MP96 and MPLC, followed by quantification in duplicate...
January 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28100306/diverse-novel-astroviruses-identified-in-wild-himalayan-marmots
#15
Yuanyun Ao, Jiemei Yu, Lili Li, Jingyuan Cao, Hongyan Deng, Yunyun Xin, Mengmeng Liu, Lin Lin, Shan Lu, Jianguo Xu, Zhaojun Duan
With advances in viral surveillance and next generation sequencing, highly diverse novel astroviruses (AstVs) and different animal hosts have been discovered in recent years. However, the existence of AstVs in marmots has yet to be shown. Here, we identified for the first time two highly divergent strains of AstVs, (tentatively named Qinghai Himalayana marmot AstV, HHMAstV1 and HHMAstV2), by viral metagenomic analysis in liver tissues isolated from wild Marmota himalayana in China. Overall, 12 of 99 (12.1%) M...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28099916/involvement-of-nf-%C3%AE%C2%BAbiz-and-related-cytokines-in-age-associated-renal-fibrosis
#16
Ki Wung Chung, Hyeong Oh Jeong, Bonggi Lee, Daeui Park, Dae Hyun Kim, Yeun Ja Choi, Eun Kyeong Lee, Kyung Mok Kim, June Whoun Park, Byung Pal Yu, Hae Young Chung
Chronic inflammation is a major contributor to age-related nephropathic changes, including renal fibrosis. In this study, various experimental paradigms were designed to delineate the role played by NF-κBIZ (also known as IκBζ) in age-associated renal fibrosis. Analyses based on RNA-sequencing findings obtained by next generation sequencing (NGS) revealed the upregulations of NF-κBIZ and of IL-6 and MCP-1 (both known to be regulated by NF-κBIZ) during aging. The up-regulation of NF-κBIZ in aged rat kidneys coincided with increased macrophage infiltration...
January 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099518/evaluation-of-methods-for-the-concentration-and-extraction-of-viruses-from-sewage-in-the-context-of-metagenomic-sequencing
#17
Mathis Hjort Hjelmsø, Maria Hellmér, Xavier Fernandez-Cassi, Natàlia Timoneda, Oksana Lukjancenko, Michael Seidel, Dennis Elsässer, Frank M Aarestrup, Charlotta Löfström, Sílvia Bofill-Mas, Josep F Abril, Rosina Girones, Anna Charlotte Schultz
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult...
2017: PloS One
https://www.readbyqxmd.com/read/28099493/different-phenotypes-of-the-two-chinese-probands-with-the-same-c-889g-a-p-c162y-mutation-in-coch-gene-verify-different-mechanisms-underlying-autosomal-dominant-nonsyndromic-deafness-9
#18
Qi Wang, Peipei Fei, Hongbo Gu, Yanmei Zhang, Xiaomei Ke, Yuhe Liu
OBJECTIVES: By analyzing the different phenotypes of two Chinese DFNA9 families with the same mutation located in the intervening region between the LCCL and vWFA domains of cochlin and testing the functional changes in the mutant cochlin, we investigated the different pathogeneses for mutations in LCCL and vWFA domains. METHODS: Targeted next-generation sequencing for deafness-related genes was used to identify the mutation in the proband in family #208. The probands of family #208 and family #32 with the same p...
2017: PloS One
https://www.readbyqxmd.com/read/28099457/comparing-and-evaluating-metagenome-assembly-tools-from-a-microbiologist-s-perspective-not-only-size-matters
#19
John Vollmers, Sandra Wiegand, Anne-Kristin Kaster
With the constant improvement in cost-efficiency and quality of Next Generation Sequencing technologies, shotgun-sequencing approaches -such as metagenomics- have nowadays become the methods of choice for studying and classifying microorganisms from various habitats. The production of data has dramatically increased over the past years and processing and analysis steps are becoming more and more of a bottleneck. Limiting factors are partly the availability of computational resources, but mainly the bioinformatics expertise in establishing and applying appropriate processing and analysis pipelines...
2017: PloS One
https://www.readbyqxmd.com/read/28099455/evaluating-the-impact-of-dna-extraction-method-on-the-representation-of-human-oral-bacterial-and-fungal-communities
#20
Anna Vesty, Kristi Biswas, Michael W Taylor, Kim Gear, Richard G Douglas
The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3-V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi...
2017: PloS One
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