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Next generation sequencing review

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https://www.readbyqxmd.com/read/29045506/clinical-and-molecular-characterization-of-patients-with-cancers-of-unknown-primary-in-the-modern-era
#1
A M Varghese, A Arora, M Capanu, N Camacho, H H Won, A Zehir, J Gao, D Chakravarty, N Schultz, D S Klimstra, M Ladanyi, D M Hyman, D B Solit, M F Berger, L B Saltz
Background: On the basis of historical data, patients with cancers of unknown primary (CUP) are generally assumed to have a dismal prognosis with overall survival of less than one year. Treatment is typically cytotoxic chemotherapy guided by histologic features and the pattern of metastatic spread. The purpose of this study was to provide a clinical and pathologic description of patients with CUP in the modern era, to define the frequency of clinically actionable molecular alterations in this population, to determine how molecular testing can alter therapeutic decisions, and to investigate novel uses of next generation sequencing in the evaluation and treatment of patients with CUP...
September 26, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29043570/towards-precision-nephrology-the-opportunities-and-challenges-of-genomic-medicine
#2
REVIEW
Jordan G Nestor, Emily E Groopman, Ali G Gharavi
The expansion of genomic medicine is furthering our understanding of many human diseases. This is well illustrated in the field of nephrology, through the characterization, discovery, and growing insight into various renal diseases through use of Next Generation Sequencing (NGS) technologies. This review will provide an overview of the diagnostic opportunities of using genetic testing in the clinical setting by describing notable discoveries regarding inherited forms of renal disease that have advanced the field and by highlighting some of the potential benefits of establishing a molecular diagnosis in a clinical practice...
October 17, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/29040360/elucidating-the-editome-bioinformatics-approaches-for-rna-editing-detection
#3
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29040208/an-update-on-gain-of-function-mutations-in-primary-immunodeficiency-diseases
#4
Rekha D Jhamnani, Sergio D Rosenzweig
PURPOSE OF REVIEW: Most primary immunodeficiencies described since 1952 were associated with loss-of-function defects. With the advent and popularization of unbiased next-generation sequencing diagnostic approaches followed by functional validation techniques, many gain-of-function mutations leading to immunodeficiency have also been identified. This review highlights the updates on pathophysiology mechanisms and new therapeutic approaches involving primary immunodeficiencies because of gain-of-function mutations...
October 16, 2017: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29039169/-prenatal-diagnosis-of-joubert-syndrome-one-case-report-and-literature-review
#5
Hong Wen, Lu Chen, Kai Yan, Jing He
A 25-year-old nulliparity underwent prenatal ultrasonography, and the fetal cerebellar abnormality was suspected. The fetal MRI showed 'molar tooth sign' in midbrain and cerebellar vermis hypoplasia. The fetal cerebellar vermis hypoplasia was confirmed by MRI imaging and autopsy after induced abortion. The next-generation sequencing showed that the fetus had a heterozygous mutation of CC2D2A gene (c.2728C > T and c.4598T > C), which might be the cause of the disease.
May 25, 2017: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
https://www.readbyqxmd.com/read/29039162/-advances-on-prenatal-diagnosis-of-birth-defects-associated-with-genetic-disorders
#6
Kai Yan, Fan Jin
Birth defects have become a major public health concern in the world, which can be resulted from the harmful environmental factors, genetic mutations or their co-effects. Prenatal diagnosis or preimplantation diagnosis has been considered as the only effective way for the prevention of the birth of those defects. Besides karyotype analysis and fluorescence in situ hybridization, chromosomal microarray analysis and next generation sequencing or its derivatives are in common use. This article reviews the advances of the newly emerging molecular techniques in prenatal diagnosis of birth defects associated with genetic disorders...
May 25, 2017: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
https://www.readbyqxmd.com/read/29037125/signature-of-genetic-associations-in-oral-cancer
#7
Vishwas Sharma, Amrita Nandan, Amitesh Kumar Sharma, Harpreet Singh, Mausumi Bharadwaj, Dhirendra Narain Sinha, Ravi Mehrotra
Oral cancer etiology is complex and controlled by multi-factorial events including genetic events. Candidate gene studies, genome-wide association studies, and next-generation sequencing identified various chromosomal loci to be associated with oral cancer. There is no available review that could give us the comprehensive picture of genetic loci identified to be associated with oral cancer by candidate gene studies-based, genome-wide association studies-based, and next-generation sequencing-based approaches...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29035510/crispri-and-crispra-screens-in-mammalian-cells-for-precision-biology-and-medicine
#8
Martin Kampmann
Next-generation DNA sequencing technologies have led to a massive accumulation of genomic and transcriptomic data from patients and healthy individuals. The major challenge ahead is to understand the functional significance of the elements of the human genome and transcriptome, and implications for diagnosis and treatment. Genetic screens in mammalian cells are a powerful approach to systematically elucidate gene function in health and disease states. In particular, recently developed CRISPR/Cas9-based screening approaches have enormous potential to uncover mechanisms and therapeutic strategies for human diseases...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29033905/a-review-on-the-applications-of-next-generation-sequencing-technologies-as-applied-to-food-related-microbiome-studies
#9
REVIEW
Yu Cao, Séamus Fanning, Sinéad Proos, Kieran Jordan, Shabarinath Srikumar
The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29031844/alternative-polyadenylation-methods-findings-and-impacts
#10
REVIEW
Wei Chen, Qi Jia, Yifan Song, Haihui Fu, Gang Wei, Ting Ni
Alternative polyadenylation (APA), a phenomenon that RNA molecules with different 3' ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells...
October 11, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29030856/mitochondrial-3-hydroxy-3-methylglutaryl-coa-synthase-deficiency-unique-presenting-laboratory-values-and-a-review-of-biochemical-and-clinical-features
#11
Erin Conboy, Filippo Vairo, Matthew Schultz, Katherine Agre, Ross Ridsdale, David Deyle, Devin Oglesbee, Dimitar Gavrilov, Eric W Klee, Brendan Lanpher
We report an 8-month-old infant with decreased consciousness after a febrile episode and reduced oral intake. He was profoundly acidotic but his lactate was normal. Serum triglycerides were markedly elevated and HDL cholesterol was very low. The urine organic acid analysis during the acute episode revealed a complex pattern of relative hypoketotic dicarboxylic aciduria, suggestive of a potential fatty acid oxidation disorder. MRI showed extensive brain abnormalities concerning for a primary energy deficiency...
October 14, 2017: JIMD Reports
https://www.readbyqxmd.com/read/29030829/review-diagnosing-common-variable-immunodeficiency-disorder-in-the-era-of-genome-sequencing
#12
REVIEW
Rohan Ameratunga, Klaus Lehnert, See-Tarn Woon, David Gillis, Vanessa L Bryant, Charlotte A Slade, Richard Steele
Common variable immunodeficiency disorders (CVID) are an enigmatic group of often heritable conditions, which may manifest for the first time in early childhood or as late as the eighth decade of life. In the last 5 years, next generation sequencing (NGS) has revolutionised identification of genetic disorders. However, despite the best efforts of researchers around the globe, CVID conditions have been slow to yield their molecular secrets. We have previously described the many clinical advantages of identifying the genetic basis of primary immunodeficiency disorders (PIDs)...
October 14, 2017: Clinical Reviews in Allergy & Immunology
https://www.readbyqxmd.com/read/29030741/the-role-of-next-generation-sequencing-in-sarcomas-evolution-from-light-microscope-to-molecular-microscope
#13
REVIEW
Roman Groisberg, Jason Roszik, Anthony Conley, Shreyaskumar R Patel, Vivek Subbiah
PURPOSE OF REVIEW: Sarcomas are rare, heterogeneous group of soft tissue and bone tumors. Precise diagnosis of specific subtypes is challenging using conventional methods. Herein, we review the role of next-generation sequencing (NGS) technology that is used for rapid sequencing of DNA and RNA. RECENT FINDINGS: Recent sarcoma specific studies recommend that molecular genetic testing should be added at diagnosis for appropriate clinical management in addition to diagnosis by expert pathologists...
October 13, 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/29028854/clinical-insights-and-emerging-strategies-in-managing-cutaneous-t-cell-lymphoma
#14
Christina C Patrone, Larisa J Geskin
<p>Mycosis Fungoides and Sézary Syndrome, the two most common types of Cutaneous T-Cell Lymphoma (CTCL), present many management challenges for dermatologists. Here, we provide a comprehensive review of up-to-date literature, guidelines, and expert clinical insights. We highlight the updates in the World Health Organization Classification of Cutaneous Lymphomas; we summarize the epidemiology, including a recently observed stabilization of increasing incidence of CTCL in the past decade and increased incidence in males, blacks, and veterans; we also provide the most recent updates on prognostic factors for CTCL...
May 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/29027628/the-prognostic-significance-of-measurable-minimal-residual-disease-in-acute-myeloid-leukemia
#15
REVIEW
Francesco Buccisano, Christopher S Hourigan, Roland B Walter
PURPOSE OF REVIEW: The purpose of this review was to evaluate recent literature on detection methodologies for, and prognostic significance of, measurable ("minimal") residual disease (MRD) in acute myeloid leukemia (AML). RECENT FINDINGS: There is no "one-fits-all" approach to MRD testing in AML. Most exploited to date are methods relying on immunophenotypic aberrancies (identified via multiparameter flow cytometry) or genetic abnormalities (identified via PCR-based assays)...
October 13, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/29027617/zebrafish-as-a-model-to-study-neuroblastoma-development
#16
REVIEW
Mattie J Casey, Rodney A Stewart
Neuroblastoma is a pediatric solid tumor arising from embryonic neural crest progenitor cells that normally generate the peripheral sympathetic nervous system. As such, the location of neuroblastoma tumors is correlated with the distribution of major post-ganglionic clusters throughout the sympathetic chain, with the highest incidence in the adrenal medulla or lumbar sympathetic ganglia (~65%). Neuroblastoma is an enigmatic tumor that can spontaneously regress with minimal treatment or become highly metastatic and develop resistance to aggressive treatments, including radiation and high-dose chemotherapy...
October 13, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/29026660/comparison-of-classical-multi-locus-sequence-typing-software-for-next-generation-sequencing-data
#17
REVIEW
Andrew J Page, Nabil-Fareed Alikhan, Heather A Carleton, Torsten Seemann, Jacqueline A Keane, Lee S Katz
Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared eight of these applications against real and simulated data, and present results on: (1) the accuracy of each method against traditional typing methods, (2) the performance on real outbreak datasets, (3) the impact of contamination and varying depth of coverage, and (4) the computational resource requirements...
August 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#18
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29023665/clinician-s-guide-to-genes-associated-with-rett-like-phenotypes-investigation-of-a-danish-cohort-and-review-of-the-literature
#19
REVIEW
Bitten Schönewolf-Greulich, Anne-Marie Bisgaard, Rikke S Møller, Morten Dunø, Karen Brøndum-Nielsen, Simran Kaur, Nicole J Van Bergen, Sebastian Lunke, Stefanie Eggers, Cathrine Jespersgaard, John Christodoulou, Zeynep Tümer
The differential diagnostics in Rett syndrome has evolved with the development of next generation sequencing based techniques and many patients have been diagnosed with other syndromes or variants in newly described genes where the associated phenotype(s) is yet to be fully explored. The term Rett-like refers to phenotypes with distinct overlapping features of Rett syndrome where the clinical criteria are not completely fulfilled. In this paper we have combined a review of Rett-like disorders with data from a Danish cohort of 35 patients with Rett-like phenotypes emphasizing the diagnostic overlap with Pitt-Hopkins syndrome, Cornelia de Lange syndrome with SMC1A variants, and epileptic encephalopathies for example due to STXBP1 variants...
October 10, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28994108/value-of-a-molecular-screening-program-to-support-clinical-trial-enrollment-in-asian-cancer-patients-the-integrated-molecular-analysis-of-cancer-imac-study
#20
Valerie Heong, Nicholas L Syn, Xiao Wen Lee, Nur Sabrina Sapari, Xue Qing Koh, Zul Fazreen Adam Isa, Joey Sy Lim, Diana Lim, Brendan Pang, Yee Liang Thian, Lai Kuan Ng, Andrea L Wong, Ross Andrew Soo, Wei Peng Yong, Cheng Ean Chee, Soo-Chin Lee, Boon-Cher Goh, Richie Soong, David S P Tan
The value of precision oncology initiatives in Asian contexts remains unresolved. Here we review the institutional implementation of prospective molecular screening to facilitate accrual of patients into biomarker-driven clinical trials, and to explore the mutational landscape of advanced tumors occurring in a prospective cohort of Asian patients (n = 396) with diverse cancer types. Next-generation sequencing (NGS) and routine clinicopathological assays such as immunohistochemistry, copy number analysis, and in situ hybridization tests were performed on tumor samples...
October 9, 2017: International Journal of Cancer. Journal International du Cancer
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