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https://www.readbyqxmd.com/read/29156800/comparative-molecular-analyses-of-left-sided-colon-right-sided-colon-and-rectal-cancers
#1
Mohamed E Salem, Benjamin A Weinberg, Joanne Xiu, Wafik S El-Deiry, Jimmy J Hwang, Zoran Gatalica, Philip A Philip, Anthony F Shields, Heinz-Josef Lenz, John L Marshall
Tumor sidedness has emerged as an important prognostic and predictive factor in the treatment of colorectal cancer. Recent studies demonstrate that patients with advanced right-sided colon cancers have a worse prognosis than those with left-sided colon or rectal cancers, and these patient subgroups respond differently to biological therapies. Historically, management of patients with metastatic colon and rectal cancers has been similar, and colon and rectal cancer patients have been grouped together in large clinical trials...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156758/development-of-novel-long-noncoding-rna-malat1-near-infrared-optical-probes-for-in-vivo-tumour-imaging
#2
Meng-Jie Dong, Cai-Qin Wang, Guo-Lin Wang, Yue-Hong Wang, Zhen-Feng Liu
With the advent of next-generation sequencing technology, there is rapidly increasing interest in long noncoding RNAs (lncRNAs). The objectives of this study were to develop a novel lncRNA MALAT1 near-infrared optical probe, to evaluate the characteristics of this optical imaging probe in vitro and to determine whether it can be used for imaging MALAT1 expression in malignant tumours in vivo. Conjugation of Cy5.5 to MALAT1 ASO was accomplished using standard NHS (N-hydroxysuccinimide) ester procedures, and the labelled MALAT1 ASO was purified with a Glen-Pak DNA Purification Cartridge and reversed-phase high performance liquid chromatography (HPLC)...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156679/remote-intracranial-recurrence-of-idh-mutant-gliomas-is-associated-with-tp53-mutations-and-an-8q-gain
#3
Shunsuke Nakae, Takema Kato, Kazuhiro Murayama, Hikaru Sasaki, Masato Abe, Masanobu Kumon, Tadashi Kumai, Kei Yamashiro, Joji Inamasu, Mitsuhiro Hasegawa, Hiroki Kurahashi, Yuichi Hirose
Most IDH mutant gliomas harbor either 1p/19q co-deletions or TP53 mutation; 1p/19q co-deleted tumors have significantly better prognoses than tumors harboring TP53 mutations. To investigate the clinical factors that contribute to differences in tumor progression of IDH mutant gliomas, we classified recurrent tumor patterns based on MRI and correlated these patterns with their genomic characterization. Accordingly, in IDH mutant gliomas (N = 66), 1p/19 co-deleted gliomas only recurred locally, whereas TP53 mutant gliomas recurred both locally and in remote intracranial regions...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156625/gene-based-pathogen-detection-can-we-use-qpcr-to-predict-the-outcome-of-diagnostic-metagenomics
#4
Sandra Christine Andersen, Mette Sofie Rousing Fachmann, Kristoffer Kiil, Eva Møller Nielsen, Jeffrey Hoorfar
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29156569/new-insights-into-the-microbiota-of-moth-pests
#5
REVIEW
Valeria Mereghetti, Bessem Chouaia, Matteo Montagna
In recent years, next generation sequencing (NGS) technologies have helped to improve our understanding of the bacterial communities associated with insects, shedding light on their wide taxonomic and functional diversity. To date, little is known about the microbiota of lepidopterans, which includes some of the most damaging agricultural and forest pests worldwide. Studying their microbiota could help us better understand their ecology and offer insights into developing new pest control strategies. In this paper, we review the literature pertaining to the microbiota of lepidopterans with a focus on pests, and highlight potential recurrent patterns regarding microbiota structure and composition...
November 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29156198/the-evolving-role-of-genomic-testing-in-assessing-prognosis-of-patients-with-myelodysplastic-syndromes
#6
REVIEW
David P Steensma
The introduction into routine hematology-oncology clinical practice of molecular genetic testing assays based on next-generation sequencing platforms is prompting reassessment of the importance of molecular assay results in comparison to existing disease-specific risk stratification tools based on clinical assessment and light microscopy. For patients with myelodysplastic syndromes (MDS), the most commonly used tools for prognostication currently include the International Prognostic Scoring System (IPSS) and the Revised IPSS (IPSS-R), which are based on marrow blast proportion, number and degree of cytopenias, and the metaphase karyotype...
December 2017: Best Practice & Research. Clinical Haematology
https://www.readbyqxmd.com/read/29156055/analysis-of-an-adtkd-family-with-a-novel-frameshift-mutation-in-muc1-reveals-characteristic-features-of-mutant-muc1-protein
#7
Satoko Yamamoto, Jun-Ya Kaimori, Takuji Yoshimura, Tomoko Namba, Atsuko Imai, Kaori Kobayashi, Ryoichi Imamura, Naotsugu Ichimaru, Kazuto Kato, Akihiro Nakaya, Shiro Takahara, Yoshitaka Isaka
Background: Medullary cystic kidney disease Type 1 is an autosomal dominant tubulointerstitial kidney disease (ADTKD). Recently, mucin 1 ( MUC1 ) was identified as a causal gene of medullary cystic kidney disease (ADTKD-MUC1). However, the MUC1 mutation was found to be a single cytosine insertion in a single copy of the GC-rich variable number of tandem repeats (VNTRs), which are very difficult to analyze by next-generation sequencing. To date, other mutations have not been detected in ADTKD-MUC1, and the mutant MUC1 protein has not been analyzed because of the difficulty of genetically modifying the VNTR sequence...
June 1, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29155849/unusual-occurrence-of-a-dag-motif-in-the-ipomovirus-cassava-brown-streak-virus-and-implications-for-its-vector-transmission
#8
Elijah Ateka, Titus Alicai, Joseph Ndunguru, Fred Tairo, Peter Sseruwagi, Samuel Kiarie, Timothy Makori, Monica A Kehoe, Laura M Boykin
Cassava is the main staple food for over 800 million people globally. Its production in eastern Africa is being constrained by two devastating Ipomoviruses that cause cassava brown streak disease (CBSD); Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), with up to 100% yield loss for smallholder farmers in the region. To date, vector studies have not resulted in reproducible and highly efficient transmission of CBSV and UCBSV. Most virus transmission studies have used Bemisia tabaci (whitefly), but a maximum of 41% U/CBSV transmission efficiency has been documented for this vector...
2017: PloS One
https://www.readbyqxmd.com/read/29155834/measuring-the-microbiome-of-chronic-wounds-with-use-of-a-topical-antimicrobial-dressing-a-feasibility-study
#9
Lindsay Kalan, Mi Zhou, Michele Labbie, Benjamin Willing
BACKGROUND: Polymicrobial communities colonize all wounds, and biofilms are hypothesized to be a key link to the chronic state and stalled healing. Molecular methods offer greater insight when studying microbial ecology in chronic wounds, as only a small fraction of wound bacteria are cultured by currently available methods and studies have shown little agreement between culture and molecular based approaches. Some interventions, like dressings with oxidized silver, are reported to help the stalled wounds move to a normal healing trajectory but the underlying mechanisms are difficult to measure...
2017: PloS One
https://www.readbyqxmd.com/read/29155823/development-and-preliminary-evaluation-of-a-multiplexed-amplification-and-next-generation-sequencing-method-for-viral-hemorrhagic-fever-diagnostics
#10
Annika Brinkmann, Koray Ergünay, Aleksandar Radonić, Zeliha Kocak Tufan, Cristina Domingo, Andreas Nitsche
BACKGROUND: We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. METHODOLOGY: An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform...
November 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#11
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155762/high-throughput-analysis-of-locomotor-behavior-in-the-drosophila-island-assay
#12
Ilse Eidhof, Michaela Fenckova, Dei M Elurbe, Bart van de Warrenburg, Anna Castells Nobau, Annette Schenck
Advances in next-generation sequencing technologies contribute to the identification of (candidate) disease genes for movement disorders and other neurological diseases at an increasing speed. However, little is known about the molecular mechanisms that underlie these disorders. The genetic, molecular, and behavioral toolbox of Drosophila melanogaster makes this model organism particularly useful to characterize new disease genes and mechanisms in a high-throughput manner. Nevertheless, high-throughput screens require efficient and reliable assays that, ideally, are cost-effective and allow for the automatized quantification of traits relevant to these disorders...
November 5, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155419/catching-hidden-variation-systematic-correction-of-reference-minor-allele-annotation-in-clinical-variant-calling
#13
Yury A Barbitoff, Igor V Bezdvornykh, Dmitrii E Polev, Elena A Serebryakova, Andrey S Glotov, Oleg S Glotov, Alexander V Predeus
PurposeWe comprehensively assessed the influence of reference minor alleles (RMAs), one of the inherent problems of the human reference genome sequence.MethodsThe variant call format (VCF) files provided by the 1000 Genomes and Exome Aggregation Consortium (ExAC) consortia were used to identify RMA sites. All coding RMA sites were checked for concordance with UniProt and the presence of same codon variants. RMA-corrected predictions of functional effect were obtained with SIFT, PolyPhen-2, and PROVEAN standalone tools and compared with dbNSFP v2...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29155047/novel-mosaic-variants-in-two-patients-with-cornelia-de-lange-syndrome
#14
Jelena Pozojevic, Ilaria Parenti, Luitgard Graul-Neumann, Sara Ruiz Gil, Erwan Watrin, Kerstin S Wendt, Ralf Werner, Tim M Strom, Gabriele Gillessen-Kaesbach, Frank J Kaiser
Cornelia de Lange syndrome (CdLS) is a dominantly inherited developmental disorder caused by mutations in genes that encode for either structural (SMC1A, SMC3, RAD21) or regulatory (NIPBL, HDAC8) subunits of the cohesin complex. NIPBL represents the major gene of the syndrome and heterozygous mutations can be identified in more than 65% of patients. Interestingly, large portions of these variants were described as somatic mosaicism and often escape standard molecular diagnostics using lymphocyte DNA. Here we discuss the role of somatic mosaicism in CdLS and describe two additional patients with NIPBL mosaicism detected by targeted gene panel or exome sequencing...
November 15, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29155022/vmg-ii-transport-medium-stabilises-oral-microbiome-samples-for-next-generation-sequencing
#15
Christina J Adler, Abbe White, Michelle Bockmann, Gina V Browne, Grant Townsend, Toby Hughes
Next-Generation Sequencing is providing insights into the critical role of the oral microbiome in dental diseases. Application of this method can require the collection of dental plaque from large cohorts in field-type conditions, which necessitates a transport medium to preserve the microbiome composition. We evaluated the use of two transport media, VMG II and RNAprotect® Bacteria Reagent (Qiagen), for room temperature storage of dental plaque. VMG II has not previously been assessed for suitability to store microbiome samples intended for deep sequencing...
November 15, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#16
REVIEW
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding, Chen Wang, Alexis B Carter
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29154802/microrna-profiling-in-mda-mb-231-human-breast-cancer-cell-exposed-to-the-phaleria-macrocarpa-boerl-fruit-ethyl-acetate-fraction-pmeaf-through-iilumina-hi-seq-technologies-and-various-in-silico-bioinformatics-tools
#17
Nowroji Kavitha, Soundararajan Vijayarathna, Shanmugapriya, Chern Ein Oon, Yeng Chen, Jagat R Kanwar, Vasu Punj, Sreenivasan Sasidharan
ETHNOPHARMACOLOGICAL RELEVANCE: Phaleria macrocarpa (Scheff) Boerl, is a famous traditional medicinal plant which exhibited cytotoxicity against various cancerous cells. Traditionally, P. macrocarpa has been used to control cancer, impotency, hemorrhoids, diabetes mellitus, allergies, liver and heart disease, kidney disorders, blood diseases, acne, stroke, migraine, and various skin diseases. AIM OF THE STUDY: Recent studies have demonstrated a potent anticancer potential of P...
November 14, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29154079/clinical-performance-of-a-next-generation-sequencing-assay-thyroseq-v2-in-the-evaluation-of-indeterminate-thyroid-nodules
#18
Aida Taye, Dillon Gurciullo, Brett A Miles, Ashita Gupta, Randall P Owen, William B Inabnet, Jessica N Beyda, Jennifer L Marti
BACKGROUND: Molecular testing with the Thyroseq v2 next generation sequencing panel ("Thyroseq") is used to estimate the risk of cancer in indeterminate thyroid nodules. METHODS: We analyzed 156 indeterminate thyroid nodules evaluated with Thyroseq, across 3 institutions. Thyroseq data and surgical pathology were matched via pathologic re-review. A result was considered Thyroseq positive if molecular alterations were annotated on the report with malignancy probability >30%...
November 16, 2017: Surgery
https://www.readbyqxmd.com/read/29153781/genetic-epidemiology-of-autosomal-recessive-hypercholesterolemia-in-sicily-identification-by-next-generation-sequencing-of-a-new-kindred
#19
Rossella Spina, Davide Noto, Carlo M Barbagallo, Roberto Monastero, Valeria Ingrassia, Vincenza Valenti, Roberta Baschi, Antonina Pipitone, Antonina Giammanco, Maria P La Spada, Gabriella Misiano, Chiara Scrimali, Angelo B Cefalù, Maurizio R Averna
BACKGROUND: Autosomal recessive hypercholesterolemia (ARH) is a rare inherited lipid disorder. In Sardinia, differently from other world regions, the mutated allele frequency is high. It is caused by mutations in the low-density lipoprotein receptor adaptor protein 1 gene. Fourteen different mutations have been reported so far; in Sardinia, 2 alleles (ARH1 and ARH2) explain most of the cases. Four ARH patients, all carriers of the ARH1 mutation, have been identified in mainland Italy and 2 in Sicily...
October 27, 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/29153744/molecular-and-functional-characterization-of-familial-chylomicronemia-syndrome
#20
Ryota Teramoto, Hayato Tada, Masa-Aki Kawashiri, Atsushi Nohara, Takuya Nakahashi, Tetsuo Konno, Akihiro Inazu, Hiroshi Mabuchi, Masakazu Yamagishi, Kenshi Hayashi
BACKGROUND AND AIMS: Familial chylomicronemia syndrome is a rare autosomal recessive disorder leading to severe hypertriglyceridemia (HTG) due to mutations in lipoprotein lipase (LPL)-associated genes. Few data exist on the clinical features of the disorder or on comprehensive genetic approaches to uncover the causative genes and mutations. METHODS: Eight patients diagnosed with familial hyperchylomicronemia with recessive inheritance were included in this study (two males and six females; median age of onset 23...
November 14, 2017: Atherosclerosis
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