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https://www.readbyqxmd.com/read/29236254/integration-of-encode-rnaseq-and-eclip-data-sets
#1
Jorge Boucas
During the last decade, the study of mRNA decay has largely benefited from an increasing number of high-throughput assays that emerged from developments in next generation sequencing (NGS) technologies as well as mass spectrometry. While assay-specific data analysis is often reported and software made available many researchers struggle with the overwhelming challenge of integrating data from diverse assays, different sources, and of different formats.We here use Python, R, and bash to analyze and integrate RNAseq and eCLIP data publicly available from ENCODE...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236251/par-clip-for-discovering-target-sites-of-rna-binding-proteins
#2
Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, Thomas Tuschl
RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A variety of experimental approaches have been developed to characterize the RNAs associated with RBPs in vitro as well as in vivo. Our laboratory developed Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP), which in combination with next-generation sequencing enables the identification of RNA targets of RBPs at a nucleotide-level resolution...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236234/assessment-of-the-functional-impact-of-germline-brca1-2-variants-located-in-non-coding-regions-in-families-with-breast-and-or-ovarian-cancer-predisposition
#3
E Santana Dos Santos, S M Caputo, L Castera, M Gendrot, A Briaux, M Breault, S Krieger, P K Rogan, E J Mucaki, L J Burke, I Bièche, C Houdayer, D Vaur, D Stoppa-Lyonnet, M A Brown, F Lallemand, E Rouleau
PURPOSE: The molecular mechanism of breast and/or ovarian cancer susceptibility remains unclear in the majority of patients. While germline mutations in the regulatory non-coding regions of BRCA1 and BRCA2 genes have been described, screening has generally been limited to coding regions. The aim of this study was to evaluate the contribution of BRCA1/2 non-coding variants. METHODS: Four BRCA1/2 non-coding regions were screened using high-resolution melting analysis/Sanger sequencing or next-generation sequencing on DNA extracted from index cases with breast and ovarian cancer predisposition (3926 for BRCA1 and 3910 for BRCA2)...
December 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29236161/genetic-analysis-of-adults-heterozygous-for-alpl-mutations
#4
Agnès Taillandier, Christelle Domingues, Annika Dufour, Françoise Debiais, Pascal Guggenbuhl, Christian Roux, Catherine Cormier, Bernard Cortet, Valérie Porquet-Bordes, Fabienne Coury, David Geneviève, Jean Chiesa, Thierry Colin, Elaine Fletcher, Agnès Guichet, Rose-Marie Javier, Michel Laroche, Michael Laurent, Ekkehart Lausch, Bruno LeHeup, Cédric Lukas, Georg Schwabe, Ineke van der Burgt, Christine Muti, Brigitte Simon-Bouy, Etienne Mornet
Hypophosphatasia (HPP) is a rare inherited metabolic bone disease due to a deficiency of the tissue nonspecific alkaline phosphatase isoenzyme (TNSALP) encoded by the ALPL gene. Patients have consistently low serum alkaline phosphatase (AP), so that this parameter is a good hallmark of the disease. Adult HPP is heterogeneous, and some patients present only mild nonpathognomonic symptoms which are also common in the general population such as joint pain, osteomalacia and osteopenia, chondrocalcinosis, arthropathy and musculoskeletal pain...
December 13, 2017: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/29234950/the-evolution-of-endometrial-carcinoma-classification-through-application-of-immunohistochemistry-and-molecular-diagnostics-past-present-and-future
#5
REVIEW
Emily A Goebel, August Vidal, Xavier Matias-Guiu, C Blake Gilks
Uterine cancer was first subclassified based on anatomic site, separating those tumours arising from the endometrium from cervical cancers. There was then further subclassification of endometrial cancers based on cell type, and this correlated with the Type I and Type II categories identified through the epidemiological studies of Bokhman, with endometrioid carcinoma corresponding (approximately) to Type I and serous carcinoma to Type II. These histotypes are not clearly separable in practice, however, with considerable interobserver variability in histotype diagnosis, especially for high-grade tumours...
December 12, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29234666/technical-advances-to-study-extracellular-vesicles
#6
REVIEW
Paula Carpintero-Fernández, Juan Fafián-Labora, Ana O'Loghlen
Extracellular vesicles are a heterogeneous and dynamic group of lipid bilayer membrane nanoparticles that can be classified into three different groups depending on their cellular origin: exosomes, microvesicles, and apoptotic bodies. They are produced by different cell types and can be isolated from almost all body fluids. EVs contain a variety of proteins, lipids, nucleic acids, and metabolites which regulate a number of biological and pathological scenarios both locally and systemically. Different techniques have been described in order to determine EV isolation, release, uptake, and cargo...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29234329/neoantigens-generated-by-individual-mutations-and-their-role-in-cancer-immunity-and-immunotherapy
#7
REVIEW
Mirjana Efremova, Francesca Finotello, Dietmar Rieder, Zlatko Trajanoski
Recent preclinical and clinical studies have proved the long-standing hypothesis that tumors elicit adaptive immune responses and that the antigens driving effective T-cell response are neoantigens, i.e., peptides that are generated from somatically mutated genes. Hence, the characterization of neoantigens and the identification of the immunogenic ones are of utmost importance for improving cancer immunotherapy and broadening its efficacy to a larger fraction of patients. In this review, we first introduce the methods used for the quantification of neoantigens using next-generation sequencing data and then summarize results obtained using these tools to characterize the neoantigen landscape in solid cancers...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29234127/recent-spread-of-varroa-destructor-virus-1-a-honey-bee-pathogen-in-the-united-states
#8
Eugene V Ryabov, Anna K Childers, Yanping Chen, Shayne Madella, Ashrafun Nessa, Dennis vanEngelsdorp, Jay D Evans
RNA viruses impact honey bee health and contribute to elevated colony loss rates worldwide. Deformed wing virus (DWV) and the closely related Varroa destructor virus-1 (VDV1), are the most widespread honey bee viruses. VDV1 is known to cause high rates of overwintering colony losses in Europe, however it was unknown in the United States (US). Using next generation sequencing, we identified VDV1 in honey bee pupae in the US. We tested 603 apiaries the US in 2016 and found that VDV1 was present in 66.0% of them, making it the second most prevalent virus after DWV, which was present in 89...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233927/comprehensive-mutation-and-copy-number-profiling-in-archived-circulating-breast-cancer-tumor-cells-documents-heterogeneous-resistance-mechanisms
#9
Costanza Paoletti, Andi K Cani, Jose M Larios, Daniel H Hovelson, Kimberly Aung, Elizabeth P Darga, Emily M Cannell, Paul J Baratta, Chia-Jen Liu, David Chu, Maryam Yazdani, Allen R Blevins, Valeria Sero, Nahomi Tokudome, Dafydd G Thomas, Christina Gersch, Anne F Schott, Yi-Mi Wu, Robert Lonigro, Dan R Robinson, Arul M Chinnaiyan, Farideh Z Bischoff, Michael D Johnson, Ben Ho Park, Daniel F Hayes, James M Rae, Scott A Tomlins
Addressing drug resistance is a core challenge in cancer research, but the degree of heterogeneity in resistance mechanisms in cancer is unclear. In this study, we conducted next-generation sequencing (NGS) of circulating tumor cells (CTC) from patients with advanced cancer, to assess mechanisms of resistance to targeted therapy and reveal opportunities for precision medicine. Comparison of the genomic landscapes of CTC and tissue metastases is complicated by challenges in comprehensive CTC genomic profiling and paired tissue acquisition, particularly in patients who progress after targeted therapy...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29233746/amino-acid-variants-of-hla-drb1-confer-susceptibility-to-dapsone-hypersensitivity-syndrome-in-addition-to-hla-b-13-01
#10
Zhenhua Yue, Yonghu Sun, Chuan Wang, Wenjun Yu, Jing Cao, Fangfang Bao, Zhenzhen Wang, Hong Liu, Furen Zhang
Dapsone hypersensitivity syndrome is a rare yet severe adverse drug reaction caused by dapsone, a principal drug in the multidrug therapy for leprosy. HLA-B*13:01 has been identified to be a strong risk factor of dapsone hypersensitivity syndrome, however its low positive predictive value indicated that additional genetic variants may involve in the disease development. To discover contributing genetic variants within HLA loci in addition to HLA-B*13:01, we performed a high coverage next-generation sequencing based HLA typing analysis in 103 dapsone-hypersensitive and 857 dapsone-tolerant HLA-B*13:01 positive leprosy patients in Chinese population...
December 9, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29233531/genomic-landscape-of-ovarian-clear-cell-carcinoma-via-whole-exome-sequencing
#11
Se Ik Kim, Ji Won Lee, Maria Lee, Hee Seung Kim, Hyun Hoon Chung, Jae-Weon Kim, Noh Hyun Park, Yong-Sang Song, Jeong-Sun Seo
OBJECTIVE: To analyze whole exome sequencing (WES) data on ovarian clear cell carcinoma (OCCC) in Korean patients via the technique of next generation sequencing (NGS). Genomic profiles were compared between endometriosis-associated OCCC (EMS-OCCC) and Non-EMS-OCCC. METHODS: We used serum samples and cancer tissues, stored at the Seoul National University Hospital Human Biobank, that were initially collected from women diagnosed with OCCC between 2012 and 2016. In total, 15 patients were enrolled: 5 with pathologically confirmed EMS-OCCC and 10 with Non-EMS-OCCC...
December 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29232946/huntingtin-polyglutamine-dependent-protein-aggregation-in-reconstituted-cells
#12
Kodai Machida, Kuru Kanzawa, Tomoaki Shigeta, Yuki Yamamoto, Kanta Tsumoto, Hiroaki Imataka
One of the aims of synthetic biology is bottom-up construction of reconstituted human cells for medical uses. To that end, we generated giant unilamella vesicles (GUVs) that contained a HeLa cell extract, which comprises a cell-free protein synthesis (CFPS) system. Then we expressed Huntingtin protein fragments that contained polyglutamine (polyQ) sequences (Htt-polyQ), a hallmark of Huntington's disease. That system produced polyQ-dependent protein aggregates, as previously demonstrated in living cells. We next simplified the system by generating GUVs that contained purified human factors, which reconstituted a CFPS system...
December 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29232568/prior-systemic-treatment-increased-the-incidence-of-somatic-mutations-in-metastatic-breast-cancer
#13
Takeo Fujii, Naoko Matsuda, Miho Kono, Kenichi Harano, Huiqin Chen, Rajyalakshmi Luthra, Sinchita Roy-Chowdhuri, Aysegul A Sahin, Chetna Wathoo, Aron Y Joon, Debu Tripathy, Funda Meric-Bernstam, Naoto T Ueno
BACKGROUND: Understanding the biology of breast cancer is important for guiding treatment strategies and revealing resistance mechanisms. Our objectives were to investigate the relationship between previous systemic therapy exposure and mutational spectrum in metastatic breast cancer and to identify clinicopathological factors associated with identified frequent somatic mutations. METHODS: Archival tissues of patients with metastatic breast cancer were subjected to hotspot molecular testing by next-generation sequencing...
December 9, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/29232328/novel-cyp2a6-diplotypes-identified-through-next-generation-sequencing-are-associated-with-in-vitro-and-in-vivo-nicotine-metabolism
#14
Julie-Anne Tanner, Andy Z Zhu, Katrina G Claw, Bhagwat Prasad, Viktoriya Korchina, Jianhong Hu, HarshaVardhan Doddapaneni, Donna M Muzny, Erin G Schuetz, Caryn Lerman, Kenneth E Thummel, Steven E Scherer, Rachel F Tyndale
OBJECTIVES: Smoking patterns and cessation rates vary widely across smokers and can be influenced by variation in rates of nicotine metabolism [i.e. cytochrome P450 2A6 (CYP2A6), enzyme activity]. There is high heritability of CYP2A6-mediated nicotine metabolism (60-80%) owing to known and unidentified genetic variation in the CYP2A6 gene. We aimed to identify and characterize additional genetic variants at the CYP2A6 gene locus. METHODS: A new CYP2A6-specific sequencing method was used to investigate genetic variation in CYP2A6...
January 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29232304/rapid-braf-mutation-tests-in-patients-with-advanced-melanoma-comparison-of-immunohistochemistry-droplet-digital-pcr-and-the-idylla-mutation-platform
#15
Cornelis Bisschop, Arja Ter Elst, Lisette J Bosman, Inge Platteel, Mathilde Jalving, Anke van den Berg, Arjan Diepstra, Bettien van Hemel, Gilles F H Diercks, Geke A P Hospers, Ed Schuuring
BRAF mutational testing has become a common practice in the diagnostic process of patients with advanced melanoma. Although time-consuming, DNA sequencing techniques are the current gold standard for mutational testing. However, in certain clinical situations, a rapid test result is required. In this study, the performance of three rapid BRAF mutation tests was compared. Thirty-nine formalin-fixed paraffin-embedded melanoma tissue samples collected between 2007 and 2014 at a single center were included. These samples were analyzed by immunohistochemistry using the anti-BRAF-V600E (VE1) mouse monocolonal antibody (BRAF-VE1 IHC), a V600E-specific Droplet Digital PCR Test, and the Idylla BRAF- Mutation Test (Idylla)...
December 11, 2017: Melanoma Research
https://www.readbyqxmd.com/read/29231896/differential-expression-of-serum-micrornas-supports-cd4%C3%A2-%C2%BA-t-cell-differentiation-into-th2-th17-cells-in-severe-equine-asthma
#16
Alicja Pacholewska, Matthias F Kraft, Vincent Gerber, Vidhya Jagannathan
MicroRNAs (miRNAs) regulate post-transcriptional gene expression and may be exported from cells via exosomes or in partnership with RNA-binding proteins. MiRNAs in body fluids can act in a hormone-like manner and play important roles in disease initiation and progression. Hence, miRNAs are promising candidates as biomarkers. To identify serum miRNA biomarkers in the equine model of asthma we investigated small RNA derived from the serum of 34 control and 37 asthmatic horses. These samples were used for next generation sequencing, novel miRNA identification and differential miRNA expression analysis...
December 12, 2017: Genes
https://www.readbyqxmd.com/read/29230833/causes-of-iron-overload-in-blood-donors-a-clinical-study
#17
A H Laursen, O W Bjerrum, L Friis-Hansen, T O Hansen, J L Marott, K Magnussen
BACKGROUND AND OBJECTIVES: Despite the obligate iron loss from blood donation, some donors present with hyperferritinaemia that can result from a wide range of acute and chronic conditions including hereditary haemochromatosis (HH). The objective of our study was to investigate the causes of hyperferritinaemia in the blood donor population and explore the value of extensive HH mutational analyses. MATERIALS AND METHODS: Forty-nine consecutive donors (f = 6, m = 43) were included prospectively from the Capital Regional Blood Center...
December 12, 2017: Vox Sanguinis
https://www.readbyqxmd.com/read/29230532/rna-mediated-transgenerational-inheritance-in-ciliates-and-plants
#18
REVIEW
Zachary T Neeb, Mariusz Nowacki
In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction...
December 11, 2017: Chromosoma
https://www.readbyqxmd.com/read/29230253/barriers-to-clinical-adoption-of-next-generation-sequencing-a-policy-delphi-panel-s-solutions
#19
Donna A Messner, Pei Koay, Jennifer Al Naber, Robert Cook-Deegan, Mary Majumder, Gail Javitt, Rachel Dvoskin, Juli Bollinger, Margaret Curnutte, Amy L McGuire
Aim: Identify solutions to the most important policy barriers to the clinical adoption of next-generation sequencing. Materials & methods: Four-round modified policy Delphi with a multistakeholder panel of 48 experts. The panel deliberated policy solutions to (previously reported) challenges deemed most important to address. Results: The group advocated using consensus panels to promote consistency in payer policies and to standardize test reporting, and favored making genomic data-sharing a condition of regulatory clearance, certification, or accreditation processes...
2017: Personalized Medicine
https://www.readbyqxmd.com/read/29230161/a-homozygous-missense-variant-in-inpp5e-associated-with-joubert-syndrome-and-related-disorders
#20
Mitesh Shetty, Nimmy Ramdas, Shubhi Sahni, Nandita Mullapudi, Sridevi Hegde
Joubert syndrome and related disorders (JSRD; ORPHA 140874) is a complex set of neurodevelopmental disorders with multiple organ involvement. JSRD is a type of ciliopathy which is caused by the presence of defective primary cilia in an individual. JSRD is commonly inherited in an autosomal recessive pattern, and more than 23 genes are known to be associated with JSRD. We report a novel homozygous mutation identified in the INPP5E gene, c.1303C>T, which leads to a change of an amino acid from arginine to tryptophan at residue 435 in the protein chain...
November 2017: Molecular Syndromology
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