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next generation sequencing analysis

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https://www.readbyqxmd.com/read/30334805/mec-misassembly-error-correction-in-contigs-based-on-distribution-of-paired-end-reads-and-statistics-of-gc-contents
#1
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/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
#2
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
#3
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/30333011/genetic-characterization-of-norovirus-gii-4-variants-circulating-in-canada-using-a-metagenomic-technique
#4
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/30332416/major-ampullate-silk-gland-transcriptomes-and-fibre-proteomes-of-the-golden-orb-weavers-nephila-plumipes-and-nephila-pilipes-araneae-nephilidae
#5
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
#6
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/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
#7
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/30326163/integrated-molecular-characterization-of-idh-mutant-glioblastomas
#8
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/30325945/de-novo-genome-and-transcriptome-analyses-provide-insights-into-the-biology-of-the-trematode-human-parasite-fasciolopsis-buski
#9
Devendra Kumar Biswal, Tanmoy Roychowdhury, Priyatama Pandey, Veena Tandon
Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perform transcriptome analysis of the giant intestinal fluke, Fasciolopsis buski, using next generation sequencing technology. Short read sequences derived from polyA containing RNA of this organism were assembled into 30,677 unigenes that led to the annotation of 12,380 genes...
2018: PloS One
https://www.readbyqxmd.com/read/30324433/identification-and-analysis-of-genes-associated-with-inherited-retinal-diseases
#10
Mubeen Khan, Zeinab Fadaie, Stéphanie S Cornelis, Frans P M Cremers, Susanne Roosing
Inherited retinal diseases (IRDs) display a very high degree of clinical and genetic heterogeneity, which poses challenges in finding the underlying defects in known IRD-associated genes and in identifying novel IRD-associated genes. Knowledge on the molecular and clinical aspects of IRDs has increased tremendously in the last decade. Here, we outline the state-of-the-art techniques to find the causative genetic variants, with special attention for next-generation sequencing which can combine molecular diagnostics and retinal disease gene identification...
2019: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30323979/plasma-pik3ca-ctdna-specific-mutation-detected-by-next-generation-sequencing-is-associated-with-clinical-outcome-in-advanced-breast-cancer
#11
Huiping Li, Yaping Xu, Fangyuan Zhao, Guohong Song, Hope S Rugo, Yan Zhang, Ling Yang, Xiaoran Liu, Bin Shao, Liang Yang, Yaxin Liu, Ran Ran, Ruyan Zhang, Yanfang Guan, Lianpeng Chang, Xin Yi
Through next generation sequencing, this study evaluated the circulating tumor DNA (ctDNA) of advanced breast cancer patients to prospectively explore the relationship between specific DNA mutations and prognosis as well as therapeutic decision making. The target region covered 1021 gene totally. Clinical characteristics, treatment and outcome data were collected. We analyzed progression-free survival (PFS) from first-line therapy and overall survival (OS), and found that their endpoints were correlated with observed gene mutations...
2018: American Journal of Cancer Research
https://www.readbyqxmd.com/read/30323313/impact-of-single-nucleotide-polymorphisms-on-p450-oxidoreductase-and-peroxisome-proliferator-activated-receptor-alpha-on-tacrolimus-pharmacokinetics-in-renal-transplant-recipients
#12
Shuhui Si, Zijie Wang, Haiwei Yang, Zhijian Han, Jun Tao, Hao Chen, Ke Wang, Miao Guo, Ruoyun Tan, Ji-Fu Wei, Min Gu
The P450 oxidoreductase (POR) and peroxisome proliferator-activated receptor alpha (PPARA) genes are associated with the activity of cytochrome P450 enzymes in vivo. We aimed to investigate the impact of single nucleotide polymorphisms (SNPs) in the POR and PPARA genes on the pharmacokinetics of tacrolimus (TAC) in renal transplant recipients. A total of 220 recipients were assessed and 105 recipients were included for final quantitative analysis. Blood samples were collected and DNA was extracted. Targeting sequencing based on next-generation sequencing was applied to detect the SNPs in the POR and PPARA genes...
October 15, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/30323237/focal-rosai-dorfman-disease-coexisting-with-lymphoma-in-the-same-anatomic-site-a-localized-histiocytic-proliferation-associated-with-mapk-erk-pathway-activation
#13
Sofia Garces, C Cameron Yin, Keyur P Patel, Joseph D Khoury, John T Manning, Shaoying Li, Jie Xu, Sergio Pina-Oviedo, Malisha R Johnson, Sergio González, Montserrat Molgó, Roberto Ruiz-Cordero, L Jeffrey Medeiros
Rosai-Dorfman disease is a rare histiocytic disorder shown to have gene mutations that activate the MAPK/ERK pathway in at least one-third of cases. Most patients with Rosai-Dorfman disease present with bulky lymphadenopathy or extranodal disease, but rarely Rosai-Dorfman disease is detected concomitantly with lymphoma in the same biopsy specimen. The underlying molecular mechanisms of focal Rosai-Dorfman disease occurring in the setting of lymphoma have not been investigated. We report 12 cases of Rosai-Dorfman disease and lymphoma involving the same anatomic site...
October 15, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/30323194/next-generation-sequencing-analysis-of-multiplex-families-with-atypical-psychosis
#14
Tatsushi Okayama, Yasuyuki Hashiguchi, Hiroki Kikuyama, Hiroshi Yoneda, Tetsufumi Kanazawa
Atypical psychosis (similar to acute and transient psychotic disorder, brief psychotic disorder) is highly heritable, but the causal genes remain unidentified. We conducted whole-genome sequencing on multiplex Japanese families with atypical psychosis. The patient group of interest shows acute psychotic features including hallucinations, delusions, and catatonic symptoms while they often show good prognosis after the onset. In addition to the next-generation analysis, HLA typing has been conveyed to check the similarity with autoimmune disease, such as systemic lupus erythematosus (SLE)...
October 15, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/30323186/discovery-of-potential-causative-mutations-in-human-coding-and-noncoding-genome-with-the-interactive-software-baseplayer
#15
Riku Katainen, Iikki Donner, Tatiana Cajuso, Eevi Kaasinen, Kimmo Palin, Veli Mäkinen, Lauri A Aaltonen, Esa Pitkänen
Next-generation sequencing (NGS) is routinely applied in life sciences and clinical practice, but interpretation of the massive quantities of genomic data produced has become a critical challenge. The genome-wide mutation analyses enabled by NGS have had a revolutionary impact in revealing the predisposing and driving DNA alterations behind a multitude of disorders. The workflow to identify causative mutations from NGS data, for example in cancer and rare diseases, commonly involves phases such as quality filtering, case-control comparison, genome annotation, and visual validation, which require multiple processing steps and usage of various tools and scripts...
October 15, 2018: Nature Protocols
https://www.readbyqxmd.com/read/30323151/analysis-of-transcriptome-sequencing-of-sciatic-nerves-in-sprague-dawley-rats-of-different-ages
#16
Jiang-Hui Liu, Qing Tang, Xiang-Xia Liu, Jian Qi, Rui-Xi Zeng, Zhao-Wei Zhu, Bo He, Yang-Bin Xu
An aging-induced decrease in Schwann cell viability can affect regeneration following peripheral nerve injury in mammals. It is therefore necessary to investigate possible age-related changes in gene expression that may affect the biological function of peripheral nerves. Ten 1-week-old and ten 12-month-old healthy male Sprague-Dawley rats were divided into young (1 week old) and adult (12 months old) groups according to their ages. mRNA expression in the sciatic nerve was compared between young and adult rats using next-generation sequencing (NGS) and bioinformatics (n = 4/group)...
December 2018: Neural Regeneration Research
https://www.readbyqxmd.com/read/30322893/identification-of-therapeutic-targets-in-chordoma-through-comprehensive-genomic-and-transcriptomic-analyses
#17
Winnie S Liang, Christopher Dardis, Adrienne Helland, Shobana Sekar, Jonathan Adkins, Lori Cuyugan, Daniel Enriquez, Sara Byron, Andrew S Little
Chordoma is a rare, orphan cancer arising from embryonal precursors of bone. Surgery and radiotherapy (RT) provide excellent local control, often at the price of significant morbidity due to the structures involved and the need for relatively high doses of RTare not typically curative; however, recurrence remains high. Although our understanding of the genetic changes that occur in chordoma is evolving rapidly, this knowledge has yet to translate into treatments. We performed comprehensive DNA (paired tumor/normal whole exome and shallow whole genome) and RNA (tumor whole transcriptome) next-generation sequencing analyses of archival sacral and clivus chordoma specimens...
October 15, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/30321633/the-mhc-in-the-era-of-next-generation-sequencing-implications-for-bridging-structure-with-function
#18
REVIEW
Effie W Petersdorf, Colm O'hUigin
The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in transplantation. Next-generation sequencing (NGS) technology has the capability of delineating the phase of variants in the HLA antigen-recognition site (ARS) with non-coding regulatory polymorphisms...
October 12, 2018: Human Immunology
https://www.readbyqxmd.com/read/30321517/intratumoral-heterogeneity-in-recurrent-metastatic-squamous-cell-carcinoma-of-the-oral-cavity-new-perspectives-afforded-by-multiregion-dna-sequencing-and-mtdna-analysis
#19
Andrea Gabusi, Davide Bartolomeo Gissi, Achille Tarsitano, Sofia Asioli, Claudio Marchetti, Lucio Montebugnoli, Maria Pia Foschini, Luca Morandi
PURPOSE: Improvements in sequencing technologies have shown that genetic differences among neoplastic cells can reflect clonal expansion. Intratumor heterogeneity (ITH) has been suggested to explain differences in prognosis and treatment response, indicating that personalized medicine is the goal of the future. This study evaluated ITH in 5 patients with recurrent metastatic oral squamous cell carcinoma (OSCC) and tracked the evolution from non-neoplastic tissue to neoplastic events developing after primary tumor formation...
September 20, 2018: Journal of Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/30321253/transcriptomics-based-identification-and-characterization-of-11-cyp450-genes-of-panax-ginseng-responsive-to-meja
#20
Xu Zeng, Tiao Luo, Jijia Li, Gui Li, Donghua Zhou, Tuo Liu, Xian Zou, Aparna Pandey, Zhiyong Luo
Cytochromes P450 (CYP450s), a superfamily of mono-oxygenases, are essential to generate highly functionalized secondary metabolites in plants and contribute to the diversification of specialized triterpenoid biosynthesis in eudicots. However, screening and identifying the exact CYP450 genes in ginsenoside biosynthesis is extremely challenging due to existence of large quantities of members in CYP450 superfamily. Therefore, to screen the CYP450 genes involved in ginsenoside biosynthesis, transcriptome dataset of Panax ginseng was created in our previous work using the technique of the next-generation sequencing...
October 15, 2018: Acta Biochimica et Biophysica Sinica
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