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Next generation sequencing review

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https://www.readbyqxmd.com/read/28344011/the-epidemiology-pathogenesis-transmission-diagnosis-and-management-of-multidrug-resistant-extensively-drug-resistant-and-incurable-tuberculosis
#1
REVIEW
Keertan Dheda, Tawanda Gumbo, Gary Maartens, Kelly E Dooley, Ruth McNerney, Megan Murray, Jennifer Furin, Edward A Nardell, Leslie London, Erica Lessem, Grant Theron, Paul van Helden, Stefan Niemann, Matthias Merker, David Dowdy, Annelies Van Rie, Gilman K H Siu, Jotam G Pasipanodya, Camilla Rodrigues, Taane G Clark, Frik A Sirgel, Aliasgar Esmail, Hsien-Ho Lin, Sachin R Atre, H Simon Schaaf, Kwok Chiu Chang, Christoph Lange, Payam Nahid, Zarir F Udwadia, C Robert Horsburgh, Gavin J Churchyard, Dick Menzies, Anneke C Hesseling, Eric Nuermberger, Helen McIlleron, Kevin P Fennelly, Eric Goemaere, Ernesto Jaramillo, Marcus Low, Carolina Morán Jara, Nesri Padayatchi, Robin M Warren
Global tuberculosis incidence has declined marginally over the past decade, and tuberculosis remains out of control in several parts of the world including Africa and Asia. Although tuberculosis control has been effective in some regions of the world, these gains are threatened by the increasing burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. XDR tuberculosis has evolved in several tuberculosis-endemic countries to drug-incurable or programmatically incurable tuberculosis (totally drug-resistant tuberculosis)...
March 15, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28337071/international-standards-for-genomes-transcriptomes-and-metagenomes
#2
Christopher E Mason, Ebrahim Afshinnekoo, Scott Tighe, Shixiu Wu, Shawn Levy
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous...
March 17, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28334283/the-microbiology-of-oil-sands-tailings-past-present-future
#3
Julia M Foght, Lisa M Gieg, Tariq Siddique
Surface mining of enormous oil sands deposits in northeastern Alberta, Canada since 1967 has contributed greatly to Canada's economy but has also received negative international attention due largely to environmental concerns and challenges. Not only have microbes profoundly affected the composition and behaviour of this petroleum resource over geological time, they currently influence the management of semi-solid tailings in oil sands tailing ponds (OSTP) and tailings reclamation. Historically, microbial impacts on OSTP were generally discounted but next-generation sequencing and biogeochemical studies have revealed unexpectedly diverse indigenous communities and expanded our fundamental understanding of anaerobic microbial functions...
March 9, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28331002/personalized-in-vitro-and-in-vivo-cancer-models-to-guide-precision-medicine
#4
Chantal Pauli, Benjamin D Hopkins, Davide Prandi, Reid Shaw, Tarcisio Fedrizzi, Andrea Sboner, Verena Sailer, Michael Augello, Loredana Puca, Rachele Rosati, Terra J McNary, Yelena Churakova, Cynthia Cheung, Joanna Triscott, David Pisapia, Rema Rao, Juan Miguel Mosquera, Brian Robinson, Bishoy M Faltas, Brooke E Emerling, Vijayakrishna K Gadi, Brady Bernard, Olivier Elemento, Himisha Beltran, Francesca Demichelis, Christopher J Kemp, Carla Grandori, Lewis C Cantley, Mark A Rubin
Precision medicine is an approach that takes into account the influence of individuals' genes, environment, and lifestyle exposures to tailor interventions. Here, we describe the development of a robust precision cancer care platform that integrates whole-exome sequencing with a living biobank that enables high-throughput drug screens on patient-derived tumor organoids. To date, 56 tumor-derived organoid cultures and 19 patient-derived xenograft (PDX) models have been established from the 769 patients enrolled in an Institutional Review Board-approved clinical trial...
March 22, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28321632/metastatic-melanoma-moves-on-translational-science-in-the-era-of-personalized-medicine
#5
Mitchell P Levesque, Phil F Cheng, Marieke I G Raaijmakers, Annalisa Saltari, Reinhard Dummer
Progress in understanding and treating metastatic melanoma is the result of decades of basic and translational research as well as the development of better in vitro tools for modeling the disease. Here, we review the latest therapeutic options for metastatic melanoma and the known genetic and non-genetic mechanisms of resistance to these therapies, as well as the in vitro toolbox that has provided the greatest insights into melanoma progression. These include next-generation sequencing technologies and more complex 2D and 3D cell culture models to functionally test the data generated by genomics approaches...
March 20, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28319011/resequencing-helminth-genomes-for-population-and-genetic-studies
#6
REVIEW
Janneke Wit, John S Gilleard
Next-generation sequencing has become increasingly accessible and economical, making genome-wide studies routine for many species, including humans, model organisms, and domestic livestock. However, in the case of helminth parasites, there are still major practical challenges to the application of these approaches for genetic and population studies. Dozens to hundreds of individual parasites from multiple populations may need to be re-sequenced which, together with the relatively large size of helminth genomes, can still make whole-genome resequencing of individual parasites unfeasible for many studies...
March 16, 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28317403/intrahepatic-cholangiocarcinoma-current-management-and-emerging-therapies
#7
Amir A Rahnemai-Azar, Allison B Weisbrod, Mary Dillhoff, Carl Schmidt, Timothy M Pawlik
Intrahepatic cholangiocarcinoma (iCCA) is a malignancy with an increasing incidence and a high-case fatality. While surgery offers the best hope at long-term survival, only one-third of tumors are amenable to surgical resection at the time of the diagnosis. Unfortunately, conventional chemotherapy offers limited survival benefit in the management of unresectable or metastatic disease. Recent advances in understanding the molecular pathogenesis of iCCA and the use of next-generation sequencing techniques have provided a chance to identify "target-able" molecular aberrations...
March 20, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28306363/genome-database-mining-for-the-discovery-of-novel-lantibiotics
#8
Stephanie K Sandiford
The effectiveness of lantibiotics against MDR pathogens and the progression of agents MU1140, NAI-107, NVB302 and duramycin into pre-clinical and clinical trials have highlighted their potential in the fight against bacterial resistance. The number of known lantibiotics and knowledge of their biosynthetic pathways has increased in recent years due to higher quality genomic data being delivered by next generation sequencing technologies combined with the development of specific genome mining tools, enabling the prediction of lantibiotic clusters...
March 17, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28303491/changing-the-therapeutic-landscape-in-non-small-cell-lung-cancers-the-evolution-of-comprehensive-molecular-profiling-improves-access-to-therapy
#9
REVIEW
Joshua K Sabari, Fernando Santini, Isabella Bergagnini, W Victoria Lai, Kathryn C Arbour, Alexander Drilon
Targeting genomic alterations has led to a paradigm shift in the treatment of patients with lung cancer. In an effort to better identify potentially actionable alterations that may predict response to FDA-approved and or investigational therapies, many centers have migrated towards performing targeted exome sequencing in patients with stage IV disease. The implementation of next-generation sequencing (NGS) in the evaluation of tumor tissue from patients with NSCLC has led to the discovery of targetable alterations in tumors that previously had no known actionable targets by less comprehensive profiling...
April 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28299199/advances-in-understanding-hypopituitarism
#10
REVIEW
Mareike R Stieg, Ulrich Renner, Günter K Stalla, Anna Kopczak
The understanding of hypopituitarism has increased over the last three years. This review provides an overview of the most important recent findings. Most of the recent research in hypopituitarism has focused on genetics. New diagnostic techniques like next-generation sequencing have led to the description of different genetic mutations causative for congenital dysfunction of the pituitary gland while new molecular mechanisms underlying pituitary ontogenesis have also been described. Furthermore, hypopituitarism may occur because of an impairment of the distinctive vascularization of the pituitary gland, especially by disruption of the long vessel connection between the hypothalamus and the pituitary...
2017: F1000Research
https://www.readbyqxmd.com/read/28298352/the-interactions-of-ants-with-their-biotic-environment
#11
EDITORIAL
Guillaume Chomicki, Susanne S Renner
This special feature results from the symposium 'Ants 2016: ant interactions with their biotic environments' held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this special feature After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28297627/clinical-and-technical-aspects-of-genomic-diagnostics-for-precision-oncology
#12
Yuri Sheikine, Frank C Kuo, Neal I Lindeman
The emergence of precision medicine has been predicated on significant recent advances in diagnostic technology, particularly the advent of next-generation sequencing (NGS). Although the chemical technology underlying NGS is complex, and the computational biology expertise required to build systems to facilely interpret the results is highly specialized, the variables involved in designing and deploying a genomic testing program for cancer can be readily understood and applied by understanding several basic considerations...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28297626/clinical-applications-of-the-genomic-landscape-of-aggressive-non-hodgkin-lymphoma
#13
Andrea B Moffitt, Sandeep S Dave
In this review, we examine the genomic landscapes of lymphomas that arise from B, T, and natural killer cells. Lymphomas represent a striking spectrum of clinical behaviors. Although some lymphomas are curable with standard therapy, the majority of the affected patients succumb to their disease. Here, the genetic underpinnings of these heterogeneous entities are reviewed. We consider B-cell lymphomas, including Burkitt lymphoma, diffuse large B-cell lymphoma, Hodgkin lymphoma, and primary mediastinal B-cell lymphoma...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28297620/germline-genetic-predisposition-to-hematologic-malignancy
#14
Elissa Furutani, Akiko Shimamura
Development of hematologic malignancies is driven by mutations that may be somatic or germline. Availability of next-generation DNA sequencing technologies has facilitated the development of individualized diagnostic evaluations and tailored treatment strategies. Until now, such personalized medical approaches have largely centered on prognostic stratification and treatment strategies informed by acquired somatic mutations. The role of germline mutations in children and adults with hematologic malignancies was previously underappreciated...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28290769/sequencing-brain-metastases-and-opportunities-for-targeted-therapies
#15
Ugonma N Chukwueke, Priscilla K Brastianos
CNS metastases have long been recognized as a common and late complication of systemic malignancies. They represent the most common tumor of the brain. As outcomes and overall survival improve with better tolerated and more durable responses from therapies for systemic cancers, the incidence and prevalence of brain metastases is likely to increase. Among the most common systemic cancers leading to brain metastases include lung, melanoma, breast (triple-negative histology) and renal cell cancers. To date, there has been infrequent involvement of gastrointestinal and gynecologic malignancies; however, this may also change, reflecting improvement in overall survival and therapeutic regimens...
March 14, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28287462/snp-discovery-using-a-pangenome-has-the-single-reference-approach-become-obsolete
#16
REVIEW
Bhavna Hurgobin, David Edwards
Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation...
March 11, 2017: Biology
https://www.readbyqxmd.com/read/28283962/update-on-the-genetics-of-dystonia
#17
REVIEW
Katja Lohmann, Christine Klein
Mainly due to the advent of next-generation sequencing (NGS), the field of genetics of dystonia has rapidly grown in recent years, which led to the discovery of a number of novel dystonia genes and the development of a new classification and nomenclature for inherited dystonias. In addition, new findings from both in vivo and in vitro studies have been published on the role of previously known dystonia genes, extending our understanding of the pathophysiology of dystonia. We here review the current knowledge and recent findings in the known genes for isolated dystonia TOR1A, THAP1, and GNAL as well as for the combined dystonias due to mutations in GCH1, ATP1A3, and SGCE...
March 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28282253/introduction-to-the-special-focus-issue-on-the-impact-of-diet-on-gut-microbiota-composition-and-function-and-future-opportunities-for-nutritional-modulation-of-the-gut-microbiome-to-improve-human-health
#18
Sharon M Donovan
Over the past decade, application of culture-independent, next generation DNA sequencing has dramatically enhanced our understanding of the composition of the gut microbiome and its association with human states of health and disease. Host genetics, age, and environmental factors such as where and who you live with, use of pre-, pro- and antibiotics, exercise and diet influence the short- and long-term composition of the microbiome. Dietary intake is a key determinant of microbiome composition and diversity and studies to date have linked long-term dietary patterns as well as short-term dietary interventions to the composition and diversity of the gut microbiome...
February 28, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28281318/intracranial-myxoid-mesenchymal-tumors-with-ewsr1-creb-family-gene-fusions-myxoid-variant-of-angiomatoid-fibrous-histiocytoma-or-novel-entity
#19
Tejus A Bale, Angelica Oviedo, Harry Kozakewich, Caterina Giannini, Phani K Davineni, Keith Ligon, Sanda Alexandrescu
BACKGROUND: Intracranial myxoid mesenchymal tumor harboring EWSR1 fusions with CREB family of genes was recently described, and it resembles the myxoid variant of angiomatoid fibrous histiocytoma. We present 3 pediatric patients with intracranial EWSR1-rearranged myxoid mesenchymal neoplasm and provide a molecular genetic characterization of these tumors. METHODS: Clinical histories and imaging results were reviewed. Histology, immunohistochemistry, EWSR1, FUS, NR4A3 fluorescence in situ hybridization (FISH), and next generation sequencing (NGS) were performed...
March 9, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28278349/beyond-the-braf-v-600e-hotspot-biology-and-clinical-implications-of-rare-braf-gene-mutations-in-melanoma-patients
#20
REVIEW
G Richtig, C Hoeller, K Kashofer, A Aigelsreiter, A Heinemann, L N Kwong, M Pichler, E Richtig
BRAF mutations can be found in approximately 50% of melanomas, whereas the most common BRAF mutation is the substitution of a valine residue at codon 600 to glutamic acid. BRAF(V)(600E) occurs in up to 95% of all melanoma cases and can be successfully blocked by using a combination of BRAF- and MEK-inhibitors. Due to the wider availability of next-generation sequencing, more non-V600 BRAF mutations are emerging, and the clinical implications of these mutations are widely unknown. In this review, we will discuss the biology of the MAPK-pathway and its different types of BRAF mutations as well as their effect on MEK activation...
March 9, 2017: British Journal of Dermatology
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