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https://www.readbyqxmd.com/read/29451897/selective-identification-of-somatic-mutations-in-pancreatic-cancer-cells-through-a-combination-of-next-generation-sequencing-of-plasma-dna-using-molecular-barcodes-and-a-bioinformatic-variant-filter
#1
Yoji Kukita, Kazuyoshi Ohkawa, Ryoji Takada, Hiroyuki Uehara, Kazuhiro Katayama, Kikuya Kato
The accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more...
2018: PloS One
https://www.readbyqxmd.com/read/29451896/hypomyelinating-disorders-in-china-the-clinical-and-genetic-heterogeneity-in-119-patients
#2
Haoran Ji, Dongxiao Li, Ye Wu, Quanli Zhang, Qiang Gu, Han Xie, Taoyun Ji, Huifang Wang, Lu Zhao, Haijuan Zhao, Yanling Yang, Hongchun Feng, Hui Xiong, Jinhua Ji, Zhixian Yang, Liping Kou, Ming Li, Xinhua Bao, Xingzhi Chang, Yuehua Zhang, Li Li, Huijuan Li, Zhengping Niu, Xiru Wu, Jiangxi Xiao, Yuwu Jiang, Jingmin Wang
OBJECTIVE: Hypomyelinating disorders are a group of clinically and genetically heterogeneous diseases characterized by neurological deterioration with hypomyelination visible on brain MRI scans. This study was aimed to clarify the clinical and genetic features of HMDs in Chinese population. METHODS: 119 patients with hypomyelinating disorders in Chinese population were enrolled and evaluated based on their history, clinical manifestation, laboratory examinations, series of brain MRI with follow-up, genetic etiological tests including chromosomal analysis, multiplex ligation probe amplification, Sanger sequencing, targeted enrichment-based next-generation sequencing and whole exome sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29451882/de-novo-transcriptomic-analysis-of-leaf-and-fruit-tissue-of-cornus-officinalis-using-illumina-platform
#3
Dian-Yun Hou, Lin-Chun Shi, Meng-Meng Yang, Jiong Li, Shuang Zhou, Hong-Xiao Zhang, Hua-Wei Xu
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization...
2018: PloS One
https://www.readbyqxmd.com/read/29451745/detection-of-ros1-positive-non-small-cell-lung-cancer-on-cytological-specimens-using-immunocytochemistry
#4
Tatjana Vlajnic, Spasenija Savic, Audrey Barascud, Betty Baschiera, Michel Bihl, Bruno Grilli, Michelle Herzog, Julien Rebetez, Lukas Bubendorf
BACKGROUND: Rearrangements of the ROS1 oncogene are found in 1% to 2% of non-small cell lung cancers (NSCLC) and are regarded as mutually exclusive oncogenic driver mutations. Since the approval of targeted therapy for ROS1-positive NSCLC, ROS1 testing has become a part of the diagnostic routine. Fluorescence in situ hybridization (FISH), optionally selected for by immunohistochemistry on histological material, is a common practice for the detection of ROS1 rearrangements. However, NSCLC often is diagnosed by cytology alone, requiring predictive marker testing on cytological specimens...
February 16, 2018: Cancer Cytopathology
https://www.readbyqxmd.com/read/29451150/identification-of-seven-novel-mutations-in-the-acid-alpha-glucosidase-gene-in-five-chinese-patients-with-late-onset-pompe-disease
#5
Hua-Xu Liu, Chuan-Qiang Pu, Qiang Shi, Yu-Tong Zhang, Rui Ban
Background: Pompe disease is a rare lysosomal glycogen storage disorder linked to the acid alpha-glucosidase gene (GAA). A wide clinical and genetic variability exists between patients from different ethnic populations, and the genotype-phenotype correlations are still not well understood. The aim of this study was to report the clinicopathological and genetic characteristics of five Chinese patients with late-onset Pompe disease (LOPD) who carried novel GAA gene mutations. Methods: Clinical and pathological data of patients diagnosed with glycogen storage disease at our institution from April 1986 to August 2017 were collected, and next-generation sequencing of frozen muscle specimens was conducted...
February 20, 2018: Chinese Medical Journal
https://www.readbyqxmd.com/read/29450879/genetic-investigation-of-93-families-with-microphthalmia-or-posterior-microphthalmos
#6
N Patel, A O Khan, S Alsahli, G Abdel-Salam, S R Nowilaty, A M Mansour, A Nabil, M Al-Owain, S Sogati, M A Salih, A M Kamal, H Alsharif, H Alsaif, S S Alzahrani, F Abdulwahab, N Ibrahim, M Hashem, T Faquih, Z A Shah, M Abouelhoda, D Monies, M Dasouki, R Shaheen, S Majid, M A Aldahmesh, F S Alkuraya
Microphthalmia is a developmental eye defect that is highly variable in severity and in its potential for systemic association. Despite the discovery of many disease genes in microphthalmia, at least 50% of patients remain undiagnosed genetically. Here, we describe a cohort of 147 patients (93 families) from our highly consanguineous population with various forms of microphthalmia (including the distinct entity of posterior microphthalmos) that were investigated using a next-generation sequencing multi-gene panel (i-panel) as well as whole exome sequencing (WES) and molecular karyotyping...
February 16, 2018: Clinical Genetics
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
#7
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/29450569/pharmacogenomics-in-diabetes-outcomes-of-thiamine-therapy-in-trma-syndrome
#8
Abdelhadi M Habeb, Sarah E Flanagan, Mohamed A Zulali, Mohamed A Abdullah, Renata Pomahačová, Veselin Boyadzhiev, Lesby E Colindres, Guillermo V Godoy, Thiruvengadam Vasanthi, Ramlah Al Saif, Aria Setoodeh, Amirreza Haghighi, Alireza Haghighi, Yomna Shaalan, Andrew T Hattersley, Sian Ellard, Elisa De Franco
AIMS/HYPOTHESIS: Diabetes is one of the cardinal features of thiamine-responsive megaloblastic anaemia (TRMA) syndrome. Current knowledge of this rare monogenic diabetes subtype is limited. We investigated the genotype, phenotype and response to thiamine (vitamin B 1 ) in a cohort of individuals with TRMA-related diabetes. METHODS: We studied 32 individuals with biallelic SLC19A2 mutations identified by Sanger or next generation sequencing. Clinical details were collected through a follow-up questionnaire...
February 15, 2018: Diabetologia
https://www.readbyqxmd.com/read/29449965/genetic-diversity-and-cross-species-transmission-of-kobuviruses-in-vietnam
#9
Lu Lu, Nguyen Van Dung, Alasdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Hong Anh, Maia A Rabaa, Ngo Tri Tue, Guy E Thwaites, Stephen Baker, Peter Simmonds, Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29449843/insights-into-the-structural-basis-of-antibody-affinity-maturation-from-next-generation-sequencing
#10
REVIEW
Arjun K Mishra, Roy A Mariuzza
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29449398/complete-genome-sequence-of-the-model-oleaginous-alga-nannochloropsis-gaditana-ccmp1894
#11
Ariel S Schwartz, Rob Brown, Imad Ajjawi, Jay McCarren, Suzan Atilla, Nick Bauman, Toby H Richardson
The model oleaginous alga Nannochloropsis gaditana was completely sequenced using a combination of optical mapping and next-generation sequencing technologies to generate one of the most complete eukaryotic genomes published to date. The assembled genome is 30.7 Mb long.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449275/circulating-tumor-dna-reveals-genetics-clonal-evolution-and-residual-disease-in-classical-hodgkin-lymphoma
#12
Valeria Spina, Alessio Bruscaggin, Annarosa Cuccaro, Maurizio Martini, Martina Di Trani, Gabriela Forestieri, Martina Manzoni, Adalgisa Condoluci, Alberto Arribas, Lodovico Terzi-Di-Bergamo, Silvia Laura Locatelli, Elisa Cupelli, Luca Ceriani, Alden A Moccia, Anastasios Stathis, Luca Nassi, Clara Deambrogi, Fary Diop, Francesca Guidetti, Alessandra Cocomazzi, Salvatore Annunziata, Vittoria Rufini, Alessandro Giordano, Antonino Neri, Renzo Boldorini, Bernhard Gerber, Francesco Bertoni, Michele Ghielmini, Georg Stüssi, Armando Santoro, Franco Cavalli, Emanuele Zucca, Luigi Maria Larocca, Gianluca Gaidano, Stefan Hohaus, Carmelo Carlo-Stella, Davide Rossi
The rarity of neoplastic cells in the biopsy imposes major technical hurdles that have so far limited genomic studies in classical Hodgkin lymphoma (cHL). By using a highly sensitive and robust deep-next-generation-sequencing approach for circulating tumor DNA (ctDNA), here we aimed at tracking the genetics of cHL in different clinical phases, and its modifications upon treatment. The analysis was based on specimens collected from 80 newly diagnosed and 32 refractory cHL patients, including longitudinal samples collected under ABVD chemotherapy and longitudinal samples from relapsing patients treated with chemotherapy and immunotherapy...
February 15, 2018: Blood
https://www.readbyqxmd.com/read/29449000/an-immunohistochemical-and-molecular-analysis-of-papillary-proliferation-of-the-endometrium
#13
Colin J R Stewart, Susan Bigby, Tino Giardina, Fabienne Grieu-Iacopetta, Benhur Amanuel
Papillary proliferations of the endometrium (PPEs) are uncommon lesions that are often associated with endometrial polyps. PPEs occasionally precede or co-exist with atypical endometrial hyperplasia or adenocarcinoma, but their pathogenesis and relationship to endometrial neoplasia is uncertain. In the present study 11 PPEs, including eight benign papillary proliferations (BPPs) and three complex papillary hyperplasias (CPHs) were examined immunohistochemically for expression of PAX2, BAF250a, p16, β-catenin and DNA mismatch repair (MMR) proteins...
February 12, 2018: Pathology
https://www.readbyqxmd.com/read/29448188/genotype-phenotype-and-in-silico-pathogenicity-analysis-of-hexb-mutations-panel-based-sequencing-for-differential-diagnosis-of-gangliosidosis
#14
Nejat Mahdieh, Sahar Mikaeeli, Ali Reza Tavasoli, Zahra Rezaei, Majid Maleki, Bahareh Rabbani
OBJECTIVES: Gangliosidosis is an inherited metabolic disorder causing neurodegeneration and motor regression. Preventive diagnosis is the first choice for the affected families due to lack of straightforward therapy. Genetic studies could confirm the diagnosis and help families for carrier screening and prenatal diagnosis. An update of HEXB gene variants concerning genotype, phenotype and in silico analysis are presented. PATIENTS AND METHODS: Panel based next generation sequencing and direct sequencing of four cases were performed to confirm the clinical diagnosis and for reproductive planning...
February 8, 2018: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/29448067/antiviral-resistance-due-to-deletion-in-the-neuraminidase-gene-and-defective-interfering-like-viral-polymerase-basic-2-rna-of-influenza-a-virus-subtype-h3n2
#15
Ramona Trebbien, Claus Bohn Christiansen, Thea Kølsen Fischer
BACKGROUND AND OBJECTIVE: Antiviral treatment of influenza virus infections can lead to drug resistance of virus. This study investigates a selection of mutations in the full genome of H3N2 influenza A virus isolated from a patient in treatment with oseltamivir. STUDY DESIGN: Respiratory samples from a patient were collected before, during, and after antiviral treatment. Whole genome sequencing of the influenza virus by next generation sequencing, and low-frequency-variant analysis was performed...
February 11, 2018: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/29447003/a-study-on-the-genetic-polymorphisms-of-cyp3a5-among-the-orang-asli-in-malaysia-using-next-generation-sequencing-platform
#16
Geik Yong Ang, Choo Yee Yu, Richard Johari James, Aminuddin Ahmad, Thuhairah Abdul Rahman, Fadzilah Mohd Nor, Syahrul Azlin Shaari, Adzrool Idzwan Ismail, Lay Kek Teh, Mohd Zaki Salleh
CYP3A5 is the predominant subfamily of biotransformation enzymes in the liver and the genetic variations in CYP3A5 are an important determinant of interindividual and interethnic differences in CYP3A-mediated drug disposition and response. This study aims to investigate the genetic polymorphisms of CYP3A5 among the Orang Asli in Peninsular Malaysia using next generation sequencing platform. Genomic DNAs were extracted from blood samples of the three main Orang Asli tribes and whole-genome sequencing was performed...
February 15, 2018: Annals of Human Biology
https://www.readbyqxmd.com/read/29446423/computational-investigation-on-dna-sequencing-using-functionalized-graphene-nanopores
#17
You-Sheng Yu, Xiang Lu, Hong-Ming Ding, Yu-Qiang Ma
Fast, low-cost and reliable DNA sequencing is one of the most desirable innovations in recent years, which can pave the way for high throughput, label-free and inexpensive personalized genome sequencing techniques. Although graphene-based nanopore devices hold great promise for next-generation DNA sequencing, it is still a challenging problem to detect different DNA sequences efficiently and accurately. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A) 20 , poly(C) 20 , poly(G) 20 , and poly(T) 20 ) through the functionalized graphene nanopores is investigated by all-atom molecular dynamic simulations...
February 15, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29445477/beta-propeller-protein-associated-neurodegeneration-a-case-report-and-review-of-the-literature
#18
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/29445422/sleeping-beauty-transposon-integrates-into-non-ta-dinucleotides
#19
Yabin Guo, Yin Zhang, Kaishun Hu
Background: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29445031/the-perils-of-single-site-genetic-testing-for-hereditary-cancer-syndromes-in-the-era-of-next-generation-sequencing
#20
Nicole Casasanta, Elizabeth Stark, Allison McHenry, Tara Biagi, Rebecca Kaltman
A challenge in counseling patients with a family history suggesting a hereditary cancer syndrome is deciding which genetic tests or panels to order. In this article, we discuss the identification of multiple familial mutations through genetic counseling and panel testing. For patients meeting National Comprehensive Cancer Network criteria for clinical genetic testing, providers should consider expanded panels to provide a more complete assessment of one's genetic risk. The continued use of expanded panel testing in the clinical setting will help inform optimal management of cancer patients, as well as the management of their unaffected family members...
February 14, 2018: Oncologist
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