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https://www.readbyqxmd.com/read/29148089/impact-of-gene-mutations-on-treatment-response-and-prognosis-of-acute-myeloid-leukemia-secondary-to-myeloproliferative-neoplasms
#1
G Venton, F Courtier, A Charbonnier, E D'Incan, C Saillard, B Mohty, M J Mozziconacci, D Birnbaum, A Murati, N Vey, J Rey
Acute myeloid leukemias secondary (sAML) to myeloproliferative neoplasms (MPN) have variable clinical courses and outcomes, but remain almost always fatal. Large cohorts of sAML to MPN are difficult to obtain and there is very little scientific literature or prospective trials for determining robust prognostic markers and efficient treatments. We analyzed event-free survival (EFS) and overall survival (OS) of 73 patients with MPN who progressed to sAML, based on their epidemiological characteristics, the preexisting MPN, the different treatments received, the different prognostic groups and the responses achieved according to the ELN, and their mutational status determined by next-generation DNA sequencing (NGS)...
November 17, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/29146476/mutation-screening-of-the-glis3-gene-in-a-cohort-of-592-chinese-patients-with-congenital-hypothyroidism
#2
Chunyun Fu, Shiyu Luo, Xigui Long, Yingfeng Li, Shangyang She, Xuehua Hu, Meizhen Mo, Zhanghong Wang, Yuhua Chen, Chun He, Jiasun Su, Yue Zhang, Fei Lin, Bobo Xie, Qifei Li, Shaoke Chen
OBJECTIVES: Defects in the human GLI-similar 3 (GLIS3) gene are reported to be a rare cause of congenital hypothyroidism (CH) and neonatal diabetes. The aim of this study was to examine the prevalence of GLIS3 mutation among CH patients in the Guangxi Zhuang Autonomous Region of China and to define the relationships between GLIS3 genotypes and clinical phenotypes. METHODS: Blood samples were collected from 592 patients with CH in Guangxi Zhuang Autonomous Region, China, and genomic DNA was extracted from peripheral blood leukocytes...
November 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29145794/analysis-of-bacterial-and-fungal-nucleic-acid-in-canine-sterile-granulomatous-and-pyogranulomatous-dermatitis-and-panniculitis
#3
Fabio B Rosa, Caitlin E Older, Courtney Meason-Smith, Jan S Suchodolski, Sonia Lingsweiler, Joanne E Mansell, Aline Rodrigues Hoffmann
Next generation sequencing (NGS) studies are revealing a diverse microbiota on the skin of dogs. The skin microbiota of canine sterile granulomatous and pyogranulomatous dermatitis (SGPD) has yet to be investigated using NGS techniques. NGS targeting the 16S rRNA and ITS-1 region of bacterial and fungal DNA, respectively, were used to investigate if bacterial and fungal DNA were associated with skin lesions in cases of canine SGPD. The study included 20 formalin-fixed paraffin-embedded (FFPE) skin samples and 12 fresh samples from SGPD-affected dogs, and 10 FFPE and 10 fresh samples from healthy dogs...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/29145603/accuracy-of-next-generation-sequencing-for-molecular-diagnosis-in-patients-with-infantile-nystagmus-syndrome
#4
John Hoon Rim, Seung-Tae Lee, Heon Yung Gee, Byung Joo Lee, Jong Rak Choi, Hye Won Park, Sueng-Han Han, Jinu Han
Importance: Infantile nystagmus syndrome (INS) is a group of disorders presenting with genetic and clinical heterogeneities that have challenged the genetic and clinical diagnoses of INS. Precise molecular diagnosis in early infancy may result in more accurate genetic counseling and improved patient management. Objective: To assess the accuracy of genomic data from next-generation sequencing (NGS) and phenotypic data to enhance the definitive diagnosis of INS. Design, Setting, and Participants: A single-center retrospective case series was conducted in 48 unrelated, consecutive patients with INS, with or without associated ocular or systemic conditions, who underwent genetic testing between June 1, 2015, and January 31, 2017...
November 16, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/29143897/anaplastic-lymphoma-kinase-testing-ihc-vs-fish-vs-ngs
#5
REVIEW
Xiaomin Niu, Jody C Chuang, Gerald J Berry, Heather A Wakelee
Personalized targeted therapy has emerged as a promising strategy in lung cancer treatment, with current attention focused on elucidation and detection of oncogenic drivers responsible for tumor initiation and maintenance and development of drug resistance. In lung cancer, several oncogenic drivers have been reported, triggering the application of tyrosine kinase inhibitors (TKIs) to target these dysfunctional genes. The anaplastic lymphoma kinase (ALK) rearrangement is responsible for about 4-7% of all non-small cell lung cancers (NSCLCs) and perhaps as high as a third in specific patient populations such as younger, male, non-smokers with advanced stage, epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene (KRAS) wild type, and signet ring cell adenocarcinoma with abundant intracytoplasmic mucin...
November 16, 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/29142766/mutations-in-nsd1-and-nfix-in-three-patients-with-clinical-features-of-sotos-syndrome-and-malan-syndrome
#6
Yongping Lu, Pin Fee Chong, Ryutaro Kira, Toshiyuki Seto, Yumiko Ondo, Keiko Shimojima, Toshiyuki Yamamoto
Mutations in nuclear receptor SET domain-containing protein 1 gene ( NSD1 ) are related to Sotos syndrome, which is characterized by overgrowth, macrocephaly, distinctive features, and neurodevelopmental disabilities. On the other hand, mutations in the nuclear factor I/X gene ( NFIX ) can lead to Malan syndrome, also known as Sotos-like syndrome, or to the Marshall-Smith syndrome. In this study, using next generation sequencing (NGS), we identified de novo mutations in NSD1 and NFIX in three patients with developmental disabilities associated with overgrowth or macrocephaly...
December 2017: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/29142287/targeted-next-generation-sequencing-in-italian-patients-with-usher-syndrome-phenotype-genotype-correlations
#7
Chiara M Eandi, Laura Dallorto, Roberta Spinetta, Maria Pia Micieli, Mario Vanzetti, Alessandro Mariottini, Ilaria Passerini, Francesca Torricelli, Camilla Alovisi, Cristiana Marchese
We report results of DNA analysis with next generation sequencing (NGS) of 21 consecutive Italian patients from 17 unrelated families with clinical diagnosis of Usher syndrome (4 USH1 and 17 USH2) searching for mutations in 11 genes: MYO7A, CDH23, PCDH15, USH1C, USH1G, USH2A, ADGVR1, DFNB31, CLRN1, PDZD7, HARS. Likely causative mutations were found in all patients: 25 pathogenic variants, 18 previously reported and 7 novel, were identified in three genes (USH2A, MYO7A, ADGRV1). All USH1 presented biallelic MYO7A mutations, one USH2 exhibited ADGRV1 mutations, whereas 16 USH2 displayed USH2A mutations...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29140551/b-cell-receptor-repertoire-sequencing-in-patients-with-primary-immunodeficiency-a-review
#8
REVIEW
Marie Ghraichy, Jacob D Galson, Dominic F Kelly, Johannes Trück
The advent of next-generation sequencing now allows a detailed assessment of the adaptive immune system in health and disease. In particular, high-throughput B-cell receptor (BCR) repertoire sequencing provides detailed information about the functionality and abnormalities of the B-cell system. However, it is mostly unknown how the BCR repertoire is altered in the context of primary immunodeficiencies (PID) and whether findings are consistent across phenotypes and genotypes. We have performed an extensive literature search of the published work on BCR repertoire sequencing in PID patients, including several forms of predominantly antibody disorders and combined immunodeficiencies...
November 15, 2017: Immunology
https://www.readbyqxmd.com/read/29139389/-ngs-to-the-rescue-of-an-atypical-case-of-alphadystroglycanopathy-with-a-lgmd-phenotype
#9
Valérie Allamand
No abstract text is available yet for this article.
November 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/29139383/-towards-a-national-standardisation-of-ngs-studies-in-the-diagnosis-of-myopathies
#10
Martin Krahn, Mathieu Cerino, Emmanuelle Campana-Salort, Mireille Cossée
No abstract text is available yet for this article.
November 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/29139381/-titin-related-muscle-disorders-an-expanding-spectrum
#11
Ana Ferreiro, J Andoni Urtizberea
Titin-related diseases of the skeletal and cardiac muscles open a new, fruitful chapter of myology. Confined for a long time to a limited number of clinical entities, the phenotypic spectrum of titinopthies is nowadays expanding rapidly together with the discovery of many pathogenic mutations of the TTN gene. Like for many genes of large size, the fine tuning and use of high-throughput sequencing (NGS) constitutes a little revolution in the field. This powerful tool allows, although with real technical hurdles, the establishment of the definite diagnosis of titinopathy...
November 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/29138120/recessive-mutation-in-tetraspanin-cd151-causes-kindler-syndrome-like-epidermolysis-bullosa-with-multi-systemic-manifestations-including-nephropathy
#12
Hassan Vahidnezhad, Leila Youssefian, Amir Hossein Saeidian, Hamid Reza Mahmoudi, Andrew Touati, Maryam Abiri, Abdol-Mohammad Kajbafzadeh, Sophia Aristodemou, Lu Liu, John A McGrath, Adam Ertel, Eric Londin, Ariana Kariminejad, Sirous Zeinali, Paolo Fortina, Jouni Uitto
Epidermolysis bullosa (EB) is caused by mutations in as many as 19 distinct genes. We have developed a next-generation sequencing (NGS) panel targeting genes known to be mutated in skin fragility disorders, including tetraspanen CD151 expressed in keratinocytes at the dermal-epidermal junction. The NGS panel was applied to a cohort of 92 consanguineous families of unknown subtype of EB. In one family, a homozygous donor splice site mutation in CD151 (NM_139029; c.351+2T>C) at the exon 5/intron 5 border was identified, and RT-PCR and whole transcriptome analysis by RNA-seq confirmed deletion of the entire exon 5 encoding 25 amino acids...
November 11, 2017: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29137436/tumor-biopsy-stratification-based-on-mtor-pathway-activity-and-functional-mutations-in-the-upstream-genes-pik3ca-and-pten
#13
Jean-François Laes, Sebastien Sauvage, Gregori Ghitti
The mechanistic target of the rapamycin (mTOR) pathway is frequently activated in human cancers. Our objective was to evaluate relationships between mTOR-pathway activity and functional mutations in the upstream genes PIK3CA and PTEN in solid-tumor biopsies from a broad selection of cancer types. Formalin-fixed paraffin-embedded (FFPE) tumor samples were analyzed by immunohistochemistry (IHC) and next-generation sequencing (NGS). TOR-pathway activation was identified by expression (by IHC) of the downstream effector p-4E-BP1...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137355/a-pilot-study-evaluating-concordance-between-blood-based-and-patient-matched-tumor-molecular-testing-within-pancreatic-cancer-patients-participating-in-the-know-your-tumor-kyt-initiative
#14
Michael J Pishvaian, R Joseph Bender, Lynn M Matrisian, Lola Rahib, Andrew Hendifar, William A Hoos, Sam Mikhail, Vincent Chung, Vincent Picozzi, Craig Heartwell, Kimberly Mason, Katelyn Varieur, Metasebia Aberra, Subha Madhavan, Emanuel Petricoin, Jonathan R Brody
Recent improvements in next-generation sequencing (NGS) technology have enabled detection of biomarkers in cell-free DNA in blood and may ultimately replace invasive tissue biopsies. However, a better understanding of the performance of blood-based NGS assays is needed prior to routine clinical use. As part of an IRB-approved molecular profiling registry trial of pancreatic ductal adenocarcinoma (PDA) patients, we facilitated blood-based NGS testing of 34 patients from multiple community-based and high-volume academic oncology practices...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137293/identification-of-novel-genetic-regulations-associated-with-airway-epithelial-homeostasis-using-next-generation-sequencing-data-and-bioinformatics-approaches
#15
Chau-Chyun Sheu, Ming-Ju Tsai, Feng-Wei Chen, Kuo-Feng Chang, Wei-An Chang, Inn-Wen Chong, Po-Lin Kuo, Ya-Ling Hsu
Airway epithelial cells play important roles in airway remodeling. Understanding gene regulations in airway epithelial homeostasis may provide new insights into pathogenesis and treatment of asthma. This study aimed to combine gene expression (GE) microarray, next generation sequencing (NGS), and bioinformatics to explore genetic regulations associated with airway epithelial homeostasis. We analyzed expression profiles of mRNAs (GE microarray) and microRNAs (NGS) in normal and asthmatic bronchial epithelial cells, and identified 9 genes with potential microRNA-mRNA interactions...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137279/implications-of-mutational-spectrum-in-myelodysplastic-syndromes-based-on-targeted-next-generation-sequencing
#16
Yuanyuan Xu, Yan Li, Qingyu Xu, Yuelong Chen, Na Lv, Yu Jing, Liping Dou, Jian Bo, Guangyuan Hou, Jing Guo, Xiuli Wang, Lili Wang, Yonghui Li, Chongjian Chen, Li Yu
Myelodysplastic syndromes (MDS) are a group of myeloid hematological malignancies, with a high risk of progression to acute myeloid leukemia (AML). To explore the role of acquired mutations in MDS, 111 MDS-associated genes were screened using next-generation sequencing (NGS), in 125 patients. One or more mutations were detected in 84% of the patients. Some gene mutations are specific for MDS and were associated with disease subtypes, and the patterns of mutational pathways could be associated with progressive MDS...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136588/a-facile-way-to-fabricate-manganese-phosphate-self-assembled-carbon-networks-as-efficient-electrochemical-catalysts-for-real-time-monitoring-of-superoxide-anions-released-from-hepg2-cells
#17
Xuan Cai, Libo Shi, Wenqian Sun, Hongli Zhao, Hong Li, Haiyan He, Minbo Lan
Quantification of superoxide anions (O2(•-)) is significant in the monitoring of many serious diseases and the design of enzyme-mimic catalysts plays the main role in the development of non-enzymatic O2(•-) sensors. Herein, we proposed a facile self-assembly process to synthesize manganese phosphate modified carbon networks using three kinds of widely-used carbon materials (MWCNTs, NGS and GO) as pillar connectors. Characterizations demonstrate that manganese phosphate is widely dispersed inside and on the surface of carbon networks without visible morphology...
November 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29136413/first-metagenomic-survey-of-the-microbial-diversity-in-bioaerosols-emitted-in-waste-sorting-plants
#18
Jodelle Degois, Frederic Clerc, Xavier Simon, Cyril Bontemps, Pierre Leblond, Philippe Duquenne
Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP)...
November 10, 2017: Annals of Work Exposures and Health
https://www.readbyqxmd.com/read/29136092/microrpm-a-microrna-prediction-model-based-only-on-plant-small-rna-sequencing-data
#19
Kuan-Chien Tseng, Yi-Fan Chiang-Hsieh, Hsuan Pai, Chi-Nga Chow, Shu-Chuan Lee, Han-Qin Zheng, Po-Li Kuo, Guan-Zhen Li, Yu-Cheng Hung, Na-Sheng Lin, Wen-Chi Chang
Motivation: MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29136087/the-utility-and-perspectives-of-ngs-based-methods-in-bsl-3-and-bsl-4-laboratory-sequencing-and-analysis-strategies
#20
Tomasz Wolkowicz
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e...
November 10, 2017: Briefings in Functional Genomics
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