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"next generation sequencing"

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https://www.readbyqxmd.com/read/30335137/identification-and-validation-of-plant-mirna-from-ngs-data-an-experimental-approach
#1
Kamalakshi Devi, Kuntal Kumar Dey, Sanjay Singh, Surajit Kumar Mishra, Mahendra Kumar Modi, Priyabrata Sen
miRNAs are class of endogenously initiated noncoding RNAs, which are most critical in gene expression and regulation at posttranscriptional level. They do so either by cleavage of the target mRNA or by translational repression. miRNAs are being given enough attention in recent years because of its role in myriad developmental processes including tumorogenesis and host-pathogen interaction. Advent of Next Generation Sequencing (NGS) technology and computational approach made it possible to pinpoint the precise role of miRNA and their target...
October 18, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/30334805/mec-misassembly-error-correction-in-contigs-based-on-distribution-of-paired-end-reads-and-statistics-of-gc-contents
#2
Binbin Wu, Min Li, Xingyu Liao, Junwei Luo, Fangxiang Wu, Yi Pan, Jianxin Wang
The de novo assembly tools aim at reconstructing genomes from next-generation sequencing (NGS) data. However, the assembly tools usually generate a large amount of contigs containing many misassemblies, which are caused by problems of repetitive regions, chimeric reads and sequencing errors. As they can improve the accuracy of assembly results, detecting and correcting the misassemblies in contigs are appealing, yet challenging. In this study, a novel method, called MEC, is proposed to identify and correct misassemblies in contigs...
October 18, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/30334804/svsr-a-program-to-simulate-structural-variations-and-generate-sequencing-reads-for-multiple-platforms
#3
Xiguo Yuan, Meihong Gao, Jun Bai, Junbo Duan
Structural variation accounts for a major fraction of mutations in the human genome and confers susceptibility to complex diseases. Next generation sequencing along with the rapid development of computational methods provides a cost-effective procedure to detect such variations. Simulation of structural variations and sequencing reads with real characteristics is essential for benchmarking the computational methods. Here, we develop a new program, SVSR, to simulate five types of structural variations (indels, tandem duplication, CNVs, inversions, and translocations) and SNPs for the human genome and to generate sequencing reads with features from popular platforms (Illumina, SOLiD, 454, and Ion Torrent)...
October 17, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/30334460/prognostic-factors-for-multiple-myeloma-in-the-era-of-novel-therapies
#4
Dimitrios C Ziogas, Meletios A Dimopoulos, Efstathios Kastritis
Multiple myeloma (MM) is characterized by notable inter-patient and intra-clonal heterogeneity that is gradually decoded over the last decade. Despite the deeper and better understanding of its biology and the development of novel therapeutic strategies that have prolonged overall survival, MM still retains a poor prognosis in patient subgroups with certain high-risk features. Areas covered: This paper summarizes currently identified features that stratified patients in high-risk myeloma with impaired prognosis and discuss available therapeutic options that may partially overcome the impact of these adverse factors in patients' outcome...
October 18, 2018: Expert Review of Hematology
https://www.readbyqxmd.com/read/30334215/a-platform-for-comprehensive-genomic-profiling-in-human-cancers-and-pharmacogenomics-therapy-selection
#5
Tadayuki Kou, Masashi Kanai, Mayumi Kamada, Masahiko Nakatsui, Shigemi Matsumoto, Yasushi Okuno, Manabu Muto
Recent innovations in next-generation sequencing (NGS) technologies have enabled comprehensive genomic profiling of human cancers in the clinical setting. The ability to profile has launched a worldwide trend known as precision medicine, and the fusion of genomic profiling and pharmacogenomics is paving the way for precision medicine for cancer. The profiling is coupled with information about chemical therapies available to patients with specific genotypes. As a result, the chemogenomic space in play is not only the standard chemical and genome space but also the mutational genome and chemical space...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30333958/the-ethnic-specific-spectrum-of-germline-nucleotide-variants-in-dna-damage-response-and-repair-genes-in-hereditary-breast-and-ovarian-cancer-patients-of-tatar-descent
#6
Olga I Brovkina, Leila Shigapova, Daria A Chudakova, Marat G Gordiev, Rafael F Enikeev, Maxim O Druzhkov, Dmitriy S Khodyrev, Elena I Shagimardanova, Alexey G Nikitin, Oleg A Gusev
The Russian population consists of more than 100 ethnic groups, presenting a unique opportunity for the identification of hereditary pathogenic mutations. To gain insight into the landscape of heredity pathogenic variants, we employed targeted next-generation sequencing to analyze the germline mutation load in the DNA damage response and repair genes of hereditary breast and ovary cancer syndrome (HBOCS) patients of Tatar ethnicity, which represents ~4% of the total Russian population. Several pathogenic mutations were identified in DNA double-strand break repair genes, and the spectrum of these markers in Tatar patients varied from that previously reported for patients of Slavic ancestry...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/30333815/a-comparison-of-techniques-for-collecting-skin-microbiome-samples-swabbing-versus-tape-stripping
#7
Kazuhiro Ogai, Satoshi Nagase, Kanae Mukai, Terumi Iuchi, Yumiko Mori, Miki Matsue, Kayo Sugitani, Junko Sugama, Shigefumi Okamoto
The swabbing and tape-stripping methods have traditionally been used for collecting skin microbiome samples for skin bacterial analysis, although no reports have compared the outcome of these methods for collecting skin bacteria. Our purpose was to show the differences in microbial composition between samples collected using the swabbing and tape-stripping methods, by both the next generation sequencing and culture studies. The skin microbiome was collected by both methods, and the samples were processed for a sequence-based microbiome analysis and culture study...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30333167/low-bias-rna-sequencing-of-the-hiv-2-genome-from-blood-plasma
#8
Katherine L James, Thushan de Silva, Katherine Brown, Hilton Whittle, Stephen Taylor, Gilean McVean, Joakim Esbjörnsson, Sarah L Rowland-Jones
Accurate determination of the genetic diversity present in the HIV quasi-species is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in co-infected subjects. The majority of traditional and next generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population...
October 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/30333011/genetic-characterization-of-norovirus-gii-4-variants-circulating-in-canada-using-a-metagenomic-technique
#9
Nicholas Petronella, Jennifer Ronholm, Menka Suresh, Jennifer Harlow, Oksana Mykytczuk, Nathalie Corneau, Sabah Bidawid, Neda Nasheri
BACKGROUND: Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome. METHOD: A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples...
October 17, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/30333000/response-to-olaparib-in-metastatic-castration-resistant-prostate-cancer-with-germline-brca2-mutation-a-case-report
#10
Yi Ma, Lijie He, Qianwen Huang, Shuang Zheng, Zhiqiang Zhang, Hongshi Li, Shuang Liu
BACKGROUND: Prostate cancer is a heterogeneous disease, meaning patients would benefit from different treatment strategies based on their molecular stratification. In recent years, several genomic studies have identified prostate cancers with defects in DNA repair genes. It is known that the PARP inhibitor, olaparib, has a significant synthetic lethal effect on tumors with BRCA 1/2 mutations, particularly in ovarian and breast cancer. CASE PRESENTATION: In this study, we describe a patient with metastatic castration-resistant prostate cancer (mCRPC) containing a BRCA2 germline mutation who underwent olaparib treatment...
October 17, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/30332963/osimertinib-quantitative-and-gene-variation-analyses-in-cerebrospinal-fluid-and-plasma-of-non-small-cell-lung-cancer-patient-with-leptomeningeal-metastases
#11
Yuanyuan Song, Peng Liu, Yu Huang, Yanfang Guan, Xiaohong Han, Yuankai Shi
BACKGROUND: Leptomeningeal metastases (LM) are much more frequent in patients of non-small lung cancer (NSCLC) harboring epidermal growth factor receptor (EGFR) mutations. Osimertinib, a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) shows promising efficacy for LM. OBJECTIVE: The aim of this study was to analyze the concentration of osimertinib and gene variation of circulating tumor DNA (ctDNA) in human plasma and cerebrospinal fluid (CSF)...
October 17, 2018: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/30332416/major-ampullate-silk-gland-transcriptomes-and-fibre-proteomes-of-the-golden-orb-weavers-nephila-plumipes-and-nephila-pilipes-araneae-nephilidae
#12
Alessandra D Whaite, Tianfang Wang, Joanne Macdonald, Scott F Cummins
Natural spider silk is one of the world's toughest proteinaceous materials, yet a truly biomimetic spider silk is elusive even after several decades of intense focus. In this study, Next-Generation Sequencing was utilised to produce transcriptomes of the major ampullate gland of two Australian golden orb-weavers, Nephila plumipes and Nephila pilipes, in order to identify highly expressed predicted proteins that may co-factor in the construction of the final polymer. Furthermore, proteomics was performed by liquid chromatography tandem-mass spectroscopy to analyse the natural solid silk fibre of each species to confirm highly expressed predicted proteins within the silk gland are present in the final silk product...
2018: PloS One
https://www.readbyqxmd.com/read/30328709/satrans-new-free-available-software-for-annotation-of-transcriptome-and-functional-analysis-of-differentially-expressed-genes
#13
Filip Zavadil Kokáš, Véronique Bergougnoux, Mária Majeská Čudejková
Recent technological advances have made next-generation sequencing (NGS) a popular and financially accessible technique allowing a broad range of analyses to be done simultaneously. A huge amount of newly generated NGS data, however, require advanced software support to help both in analyzing the data and biologically interpreting the results. In this article, we describe SATrans (Software for Annotation of Transcriptome), a software package providing fast and robust functional annotation of novel sequences obtained from transcriptome sequencing...
October 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/30328534/current-use-and-promise-of-urinary-markers-for-urothelial-cancer
#14
REVIEW
William Tabayoyong, Ashish M Kamat
PURPOSE OF REVIEW: We summarize the current literature regarding the available urinary biomarkers for the detection and surveillance of bladder cancer. RECENT FINDINGS: Four urinary biomarkers have FDA approval for the detection of bladder cancer; however, they have not supplanted cystoscopy and urine cytology as the gold standard. Recent technological advances in next-generation sequencing have allowed the field of urinary biomarker research to move beyond protein biomarkers and now include genomic, transcriptomic, and epigenetic panels...
October 17, 2018: Current Urology Reports
https://www.readbyqxmd.com/read/30327352/clonoseq-cleared-for-residual-cancer-testing
#15
(no author information available yet)
The FDA granted marketing authorization to the first-ever next-generation sequencing assay for detecting minimal residual disease in patients with acute lymphoblastic leukemia or multiple myeloma.
October 16, 2018: Cancer Discovery
https://www.readbyqxmd.com/read/30327302/pten-expression-not-mutation-status-for-tsc1-tsc2-or-mtor-correlates-with-outcome-on-everolimus-in-patients-with-renal-cell-carcinoma-treated-on-record-3
#16
Martin H Voss, David Chen, Albert Reising, Mahtab Marker, Jiayuan Shi, Jianing Xu, Irina Ostrovnaya, Venkatraman Seshan, Almedina Redzematovic, Ying-Bei Chen, Parul Patel, Xia Han, James J Hsieh, A Ari Hakimi, Robert J Motzer
PURPOSE: Genomic alterations in key components of PI3K/mTOR pathway have been proposed as candidate predictive markers for rapalog therapy in renal cell carcinoma (RCC). We tested this hypothesis in patients from a randomized phase 2 trial of everolimus vs sunitinib. EXPERIMENTAL DESIGN: Archival specimens collected at baseline were analyzed with targeted next-generation sequencing (NGS). Focus of interest were alterations in key PI3K pathway components. PTEN expression was assessed by immunohistochemistry (IHC)...
October 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/30326846/devicnv-detection-and-visualization-of-exon-level-copy-number-variants-in-targeted-next-generation-sequencing-data
#17
Yeeok Kang, Seong-Hyeuk Nam, Kyung Sun Park, Yoonjung Kim, Jong-Won Kim, Eunjung Lee, Jung Min Ko, Kyung-A Lee, Inho Park
BACKGROUND: Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests. RESULTS: We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample...
October 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/30326163/integrated-molecular-characterization-of-idh-mutant-glioblastomas
#18
Andrey Korshunov, Belen Casalini, Lukas Chavez, Thomas Hielscher, Martin Sill, Marina Ryzhova, Tanvi Sharma, Daniel Schrimpf, Damian Stichel, David Capper, David E Reuss, Dominik Sturm, Oxana Absalyamova, Andrey Golanov, Sander Lambo, Melanie Bewerunge-Hudler, Peter Lichter, Christel Herold-Mende, Wolfgang Wick, Stefan M Pfister, Marcel Kool, David T W Jones, Andreas von Deimling, Felix Sahm
AIMS: Mutations of isocitrate dehydrogenase (IDH)1/2 affect almost all astrocytomas of WHO grade II and III. A subset of IDH-mutant astrocytic tumours progresses to IDH-mutant glioblastoma or presents with the histology of a glioblastoma at first presentation. We set out here to assess the molecular spectrum of IDH-mutant glioblastomas. METHODS: We performed an integrated molecular analysis of a mono-centric cohort (n = 97); assessed through genome-wide DNA methylation analysis, copy-number profiling, and targeted next generation sequencing using a neurooncology-tailored gene panel...
October 16, 2018: Neuropathology and Applied Neurobiology
https://www.readbyqxmd.com/read/30325996/plasma-vs-tissue-next-generation-sequencing-in-non-small-cell-lung-cancer-either-both-or-neither
#19
Bishal Gyawali, Howard Jack West
No abstract text is available yet for this article.
October 11, 2018: JAMA Oncology
https://www.readbyqxmd.com/read/30325992/clinical-implications-of-plasma-based-genotyping-with-the-delivery-of-personalized-therapy-in-metastatic-non-small-cell-lung-cancer
#20
Charu Aggarwal, Jeffrey C Thompson, Taylor A Black, Sharyn I Katz, Ryan Fan, Stephanie S Yee, Austin L Chien, Tracey L Evans, Joshua M Bauml, Evan W Alley, Christine A Ciunci, Abigail T Berman, Roger B Cohen, David B Lieberman, Krishna S Majmundar, Samantha L Savitch, Jennifer J D Morrissette, Wei-Ting Hwang, Kojo S J Elenitoba-Johnson, Corey J Langer, Erica L Carpenter
Importance: The clinical implications of adding plasma-based circulating tumor DNA next-generation sequencing (NGS) to tissue NGS for targetable mutation detection in non-small cell lung cancer (NSCLC) have not been formally assessed. Objective: To determine whether plasma NGS testing was associated with improved mutation detection and enhanced delivery of personalized therapy in a real-world clinical setting. Design, Setting, and Participants: This prospective cohort study enrolled 323 patients with metastatic NSCLC who had plasma testing ordered as part of routine clinical management...
October 11, 2018: JAMA Oncology
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