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Next generation sequencing review

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https://www.readbyqxmd.com/read/29471208/understanding-biopharmaceutical-production-at-single-nucleotide-resolution-using-ribosome-footprint-profiling
#1
REVIEW
Ioanna Tzani, Craig Monger, Paul Kelly, Niall Barron, Ronan M Kelly, Colin Clarke
Biopharmaceuticals such as monoclonal antibodies have revolutionised the treatment of a variety of diseases. The production of recombinant therapeutic proteins, however, remains expensive due to the manufacturing complexity of mammalian expression systems and the regulatory burden associated with administrating these medicines to patients in a safe and efficacious manner. In recent years, academic and industrial groups have begun to develop a greater understanding of the biology of host cell lines, such as Chinese hamster ovary (CHO) cells and utilise that information for process development and cell line engineering...
February 19, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29470720/diagnostic-tools-for-inborn-errors-of-human-immunity-primary-immunodeficiencies-and-immune-dysregulatory-diseases
#2
REVIEW
Annely M Richardson, Ann M Moyer, Linda Hasadsri, Roshini S Abraham
PURPOSE OF REVIEW: The purpose of this review is to provide an overview of diagnostic testing in primary immunodeficiency and immune dysregulatory disorders (PIDDs), particularly focusing on flow cytometry and genetic techniques, utilizing specific examples of PIDDs. RECENT FINDINGS: Flow cytometry remains a vital tool in the diagnosis and monitoring of immunological diseases. Its utility ranges from cellular analysis and specific protein quantitation to functional assays and signaling pathway analysis...
February 22, 2018: Current Allergy and Asthma Reports
https://www.readbyqxmd.com/read/29468924/emerging-molecular-target-antagonists-for-the-treatment-of-biliary-tract-cancer
#3
Pasquale Lombardi, Donatella Marino, Elisabetta Fenocchio, Giovanna Chilà, Massimo Aglietta, Francesco Leone
Biliary tract cancers (BTCs) are a heterogeneous group of cancers, characterized by low incidence but poor prognosis. Even after complete surgical resection for early stage, relapse is frequent and the lack of effective treatments contributes to the dismal prognosis. To date, the only standard treatment in first-line is cisplatin/gemcitabine combination, whereas no standard in 2nd -line has been defined. Hence, the current goal is to better understand the biology of BTCs, discovering new treatment methods and improving clinical outcomes...
February 22, 2018: Expert Opinion on Emerging Drugs
https://www.readbyqxmd.com/read/29467791/next-generation-sequencing-methods-for-diagnosis-of-epilepsy-syndromes
#4
REVIEW
Paul Dunn, Cassie L Albury, Neven Maksemous, Miles C Benton, Heidi G Sutherland, Robert A Smith, Larisa M Haupt, Lyn R Griffiths
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29465426/advances-in-molecular-diagnosis-and-therapeutics-in-nephrotic-syndrome-and-focal-and-segmental-glomerulosclerosis
#5
Bedra Sharif, Moumita Barua
PURPOSE OF REVIEW: The widespread adoption of next-generation sequencing by research and clinical laboratories has begun to uncover the previously unknown genetic basis of many diseases. In nephrology, one of the best examples of this is seen in focal and segmental glomerulosclerosis (FSGS) and nephrotic syndrome. We review advances made in 2017 as a result of human and molecular genetic studies as it relates to FSGS and nephrotic syndrome. RECENT FINDINGS: There are more than 50 monogenic genes described in steroid-resistant nephrotic syndrome and FSGS, with seven reported in 2017...
February 19, 2018: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/29464738/heterozygous-aggrecan-variants-are-associated-with-short-stature-and-brachydactyly-description-of-16-probands-and-a-review-of-the-literature
#6
Lucía Sentchordi-Montané, Miriam Aza-Carmona, Sara Benito-Sanz, Ana C Barreda-Bonis, Consuelo Sánchez-Garre, Pablo Prieto-Matos, Pablo Ruiz-Ocaña, Alfonso Lechuga-Sancho, Atilano Carcavilla-Urquí, Inés Mulero-Collantes, Gabriel A Martos-Moreno, Angela Del Pozo, Elena Vallespín, Amaka Offiah, Manuel Parrón-Pajares, I Dinis, Sergio B Sousa, Purificación Ros-Pérez, Isabel González-Casado, Karen E Heath
OBJECTIVE: Mutations in the aggrecan gene (ACAN) have been identified in two autosomal dominant skeletal dysplasias, Spondyloepiphyseal dysplasia, Kimberley type (SEDK) and osteochondritis dissecans, as well as in a severe recessive dysplasia, Spondyloepimetaphyseal dysplasia, aggrecan type. Next generation sequencing (NGS) has aided the identification of heterozygous ACAN mutations in individuals with short stature, minor skeletal defects and mild facial dysmorphisms, some of whom have advanced bone age (BA), poor pubertal spurt and early growth cessation as well as precocious osteoarthritis...
February 21, 2018: Clinical Endocrinology
https://www.readbyqxmd.com/read/29464508/long-noncoding-rnas-new-players-in-the-osteogenic-differentiation-of-bone-marrow-and-adipose-derived-mesenchymal-stem-cells
#7
REVIEW
Qiaolin Yang, Lingfei Jia, Xiaobei Li, Runzhi Guo, Yiping Huang, Yunfei Zheng, Weiran Li
Mesenchymal stem cells (MSCs) are an important population of multipotent stem cells that differentiate into multiple lineages and display great potential in bone regeneration and repair. Although the role of protein-coding genes in the osteogenic differentiation of MSCs has been extensively studied, the functions of noncoding RNAs in the osteogenic differentiation of MSCs are unclear. The recent application of next-generation sequencing to MSC transcriptomes has revealed that long noncoding RNAs (lncRNAs) are associated with the osteogenic differentiation of MSCs...
February 20, 2018: Stem Cell Reviews
https://www.readbyqxmd.com/read/29450850/recurrent-fever-and-arthralgia-as-the-presentation-of-tumor-necrosis-factor-receptor-associated-periodic-syndrome-traps-in-a-chinese-girl-a-case-report-and-review-of-the-literature
#8
REVIEW
Yanxia Chen, Xingqi Huang, Sujie Zheng, Zhongliang Zhu, Wei Yang, Jinlin Liu
Tumor necrosis factor receptor-associated periodic syndrome (TRAPS) is characterized by recurrent episodes of inflammation with fever, abdominal pain, chest pain, rash, myalgia, arthralgia, conjunctivitis, and periorbital edema. This condition is a rare autosomal dominant disease that is strongly associated with heterozygous mutations in the tumor necrosis factor (TNF) receptor super family 1A (TNFRSF1A) gene. This condition is believed to be more common in Western countries than in Asian countries, and the AA amyloidosis rate for European countries is estimated to be 10%...
February 15, 2018: Clinical Rheumatology
https://www.readbyqxmd.com/read/29445477/beta-propeller-protein-associated-neurodegeneration-a-case-report-and-review-of-the-literature
#9
Kjersti Eline Stige, Ivar Otto Gjerde, Gunnar Houge, Per Morten Knappskog, Charalampos Tzoulis
Beta-propeller protein-associated neurodegeneration (BPAN) is a rare disorder, which is increasingly recognized thanks to next-generation sequencing. Due to a highly variable phenotype, patients may present to pediatrics, neurology, psychiatry, or internal medicine. It is therefore essential that physicians of different specialties are familiar with this severe and debilitating condition.
February 2018: Clinical Case Reports
https://www.readbyqxmd.com/read/29438290/mining-and-development-of-novel-ssr-markers-using-next-generation-sequencing-ngs-data-in-plants
#10
REVIEW
Sima Taheri, Thohirah Lee Abdullah, Mohd Rafii Yusop, Mohamed Musa Hanafi, Mahbod Sahebi, Parisa Azizi, Redmond Ramin Shamshiri
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development...
February 13, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29433547/finite-size-effects-in-transcript-sequencing-count-distribution-its-power-law-correction-necessarily-precedes-downstream-normalization-and-comparative-analysis
#11
Wing-Cheong Wong, Hong-Kiat Ng, Erwin Tantoso, Richie Soong, Frank Eisenhaber
BACKGROUND: Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i...
February 12, 2018: Biology Direct
https://www.readbyqxmd.com/read/29432242/epileptic-encephalopathies
#12
Shaun A Hussain
PURPOSE OF REVIEW: This article reviews the manifestations and treatment of the epileptic encephalopathies, which are a heterogeneous group of disorders characterized by both seizures and neurocognitive impairment. RECENT FINDINGS: Next-generation (exome- and genome-based) sequencing technologies are revolutionizing the identification of single-gene causes of epileptic encephalopathy but have only had a modest impact on patient-specific treatment decisions. The treatment of most forms of epileptic encephalopathy remains a particularly challenging endeavor, with therapeutic decisions chiefly driven by the electroclinical syndrome classification...
February 2018: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/29432238/nervous-system-malformations
#13
John Gaitanis, Tomo Tarui
PURPOSE OF REVIEW: This article provides an overview of the most common nervous system malformations and serves as a reference for the latest advances in diagnosis and treatment. RECENT FINDINGS: Major advances have occurred in recognizing the genetic basis of nervous system malformations. Environmental causes of nervous system malformations, such as perinatal infections including Zika virus, are also reviewed. Treatment for nervous system malformations begins prior to birth with prevention...
February 2018: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/29432235/genetic-diagnostics-for-neurologists
#14
Laura Silveira-Moriyama, Alex R Paciorkowski
PURPOSE OF REVIEW: This article puts advances in the field of neurogenetics into context and provides a quick review of the broad concepts necessary for current practice in neurology. RECENT FINDINGS: The exponential growth of genetic testing is due to its increased speed and decreasing cost, and it is now a routine part of the clinical care for a number of neurologic patients. In addition, phenotypic pleiotropy (mutations in the same gene causing very disparate phenotypes) and genetic heterogeneity (the same clinical phenotype resulting from mutations in different genes) are now known to exist in a number of conditions, adding an additional layer of complexity for genetic testing in these disorders...
February 2018: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/29429353/-evolution-of-molecular-genetic-methods-in-the-clinical-diagnosis-of-hereditary-endocrine-tumour-syndromes
#15
Balázs Sarkadi, Vince Kornél Grolmusz, Henriett Butz, Annamária Kövesdi, István Likó, Gábor Nyirő, Péter Igaz, Attila Patócs
The common features of hereditary endocrine tumour syndromes or multiple endocrine neoplasias (MEN) are the association of various tumours of different endocrine organs in one patient or within the same family. Different types can be distinguished from among which type 1 and type 2 are the most common. The mode of inheritance is autosomal dominant, meaning that there is a 50% chance to inherit the pathogenic alteration. The pathogenic variants of genes responsible for MEN syndromes have also been identified in sporadic endocrine tumours and many cases initially referred to as sporadic have been later categorized as familiar based on genetic analysis...
February 2018: Orvosi Hetilap
https://www.readbyqxmd.com/read/29429202/-cilia-ultrastructural-and-gene-variation-of-primary-ciliary-dyskinesia-report-of-three-cases-and-literatures-review
#16
K Wang, X Chen, C Y Guo, F Q Liu, J R Wang, L F Sun
Objective: To analyze the clinical manifestations, cilia ultrastructure and gene variations of primary ciliary dyskinesia (PCD). Methods: Analysis of three cases diagnosed as PCD by transmission electron microscopy of the endobronchial biopsy material in Division of Pediatric Pulmonology of Shandong Provincial Hospital between 2013 and 2016. Target gene sequence capture and next generation sequencing were used to analyze the gene. Related literatures on gene variation of PCD in Chinese were reviewed from Online Mendelian Inheritance in Man, Human Gene Mutation Database, PubMed and CNKI up to July 2017 by using search terms of "PCD" , "gene" , "Chinese"...
February 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29426776/therapeutic-implications-of-the-gastrointestinal-microbiome
#17
REVIEW
Purna C Kayshap, Eamonn Mm Quigley
Gut microbiome is an integral part of the metabolic machinery that contributes to normal host function. The advent of next generation sequencing technologies has allowed an in-depth investigation of the microbiome at various body sites including microbes which are challenging to culture. The same technologies have revealed the metabolic capacity of the microbiome, identified novel microbial products and suggested possible implications for human health. The gut microbiome has previously not been considered in aspects of human health such as response to medications, which may be metabolized to a varying extent by the microbiome, thereby, altering their efficacy and the incidence of adverse events...
February 6, 2018: Current Opinion in Pharmacology
https://www.readbyqxmd.com/read/29426337/non-coding-rnas-and-retroviruses
#18
REVIEW
Xu Zhang, Xiancai Ma, Shuliang Jing, Hui Zhang, Yijun Zhang
Retroviruses can cause severe diseases such as cancer and acquired immunodeficiency syndrome. A unique feature in the life cycle of retroviruses is that their RNA genome is reverse transcribed into double-stranded DNA, which then integrates into the host genome to exploit the host machinery for their benefits. The metazoan genome encodes numerous non-coding RNAs (ncRNA), which act as key regulators in essential cellular processes such as antiviral response. The development of next-generation sequencing technology has greatly accelerated the detection of ncRNAs from viruses and their hosts...
February 9, 2018: Retrovirology
https://www.readbyqxmd.com/read/29424002/perpetual-complexity-predicting-human-cd8-t-cell-responses-to-pathogenic-peptides
#19
REVIEW
Anthony R Di Carluccio, Cristina F Triffon, Weisan Chen
The accurate prediction of human CD8+ T cell epitopes has great potential clinical and translational implications in the context of infection, cancer and autoimmunity. Prediction algorithms have traditionally focused on calculated peptide affinity for the binding groove of MHC-I. However, over the years it has become increasingly clear that the ultimate T cell recognition of MHC-I-bound peptides is governed by many contributing factors within the complex antigen presentation pathway. Recent advances in next-generation sequencing and immunnopeptidomics have increased the precision of HLA-I sub-allele classification, and have led to the discovery of peptide processing events and individual allele-specific binding preferences...
February 9, 2018: Immunology and Cell Biology
https://www.readbyqxmd.com/read/29422440/gyg1-causing-progressive-limb-girdle-myopathy-with-onset-during-teenage-years-polyglucosan-body-myopathy-2
#20
Mahalekshmi Desikan, Renata Siciliani Scalco, Andreea Manole, Alice R Gardiner, Anthony H Schapira, Robin H Lachmann, Henry Houlden, Janice L Holton, Rahul Phadke, Ros Quinlivan
An 84-year-old lady with slowly progressive limb and axial muscle weakness with onset in her teens was referred for genetic investigations. Targeted next generation sequencing (NGS) revealed a homozygous mutation GYG1 in exon5:c.487delG:p.D163fs, confirming the diagnosis of Polyglucosan Body Myopathy 2 (PGBM2). Retrospective review of muscle pathology revealed a florid vacuolar myopathy with histochemical and ultrastructural features consistent with a polyglucosan storage myopathy. No cardiac symptoms were reported...
January 10, 2018: Neuromuscular Disorders: NMD
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