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Whole genome alignment

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https://www.readbyqxmd.com/read/29327207/phenotypic-and-functional-characteristics-of-human-schwann-cells-as-revealed-by-cell-based-assays-and-rna-seq
#1
Paula V Monje, David Sant, Gaofeng Wang
This study comprehensively addresses the phenotype, function, and whole transcriptome of primary human and rodent Schwann cells (SCs) and highlights key species-specific features beyond the expected donor variability that account for the differential ability of human SCs to proliferate, differentiate, and interact with axons in vitro. Contrary to rat SCs, human SCs were insensitive to mitogenic factors other than neuregulin and presented phenotypic variants at various stages of differentiation, along with a mixture of proliferating and senescent cells, under optimal growth-promoting conditions...
January 11, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29320538/germline-and-somatic-variant-identification-using-bgiseq-500-and-hiseq-x-ten-whole-genome-sequencing
#2
Ann-Marie Patch, Katia Nones, Stephen H Kazakoff, Felicity Newell, Scott Wood, Conrad Leonard, Oliver Holmes, Qinying Xu, Venkateswar Addala, Jenette Creaney, Bruce W Robinson, Shujin Fu, Chunyu Geng, Tong Li, Wenwei Zhang, Xinming Liang, Junhua Rao, Jiahao Wang, Mingyu Tian, Yonggang Zhao, Fei Teng, Honglan Gou, Bicheng Yang, Hui Jiang, Feng Mu, John V Pearson, Nicola Waddell
Technological innovation and increased affordability have contributed to the widespread adoption of genome sequencing technologies in biomedical research. In particular large cancer research consortia have embraced next generation sequencing, and have used the technology to define the somatic mutation landscape of multiple cancer types. These studies have primarily utilised the Illumina HiSeq platforms. In this study we performed whole genome sequencing of three malignant pleural mesothelioma and matched normal samples using a new platform, the BGISEQ-500, and compared the results obtained with Illumina HiSeq X Ten...
2018: PloS One
https://www.readbyqxmd.com/read/29304755/computational-approach-to-discriminate-human-and-mouse-sequences-in-patient-derived-tumour-xenografts
#3
Maurizio Callari, Ankita Sati Batra, Rajbir Nath Batra, Stephen-John Sammut, Wendy Greenwood, Harry Clifford, Colin Hercus, Suet-Feung Chin, Alejandra Bruna, Oscar M Rueda, Carlos Caldas
BACKGROUND: Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. RESULTS: In this study we generated Whole Exome Sequencing (WES), Reduced Representation Bisulfite Sequencing (RRBS) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA and from a cohort of human breast cancers and their derived PDTXs...
January 5, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29297318/16spip-a-comprehensive-analysis-pipeline-for-rapid-pathogen-detection-in-clinical-samples-based-on-16s-metagenomic-sequencing
#4
Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li, Wen Zhang
BACKGROUND: Pathogen detection in clinical samples based on 16S metagenomic sequencing technology in microbiology laboratories is an important strategy for clinical diagnosis, public health surveillance, and investigations of outbreaks. However, the implementation of the technology is limited by its accuracy and the time required for bioinformatics analysis. Therefore, a simple, standardized, and rapid analysis pipeline from the receipt of clinical samples to the generation of a test report is needed to increase the use of metagenomic analyses in clinical settings...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29277875/bioinformatic-approaches-for-comparative-analysis-of-viruses
#5
Deyvid Amgarten, Chris Upton
The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29277866/comparative-genome-annotation
#6
Stefanie König, Lars Romoth, Mario Stanke
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. Increasingly, such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29259599/epidemiology-of-danish-aeromonas-salmonicida-subsp-salmonicida-in-fish-farms-using-whole-genome-sequencing
#7
Simona Bartkova, Pimlapas Leekitcharoenphon, Frank M Aarestrup, Inger Dalsgaard
Furunculosis, a serious infection caused by the bacterium Aeromonas salmonicida subsp. salmonicida is common in sea-reared rainbow trout production in Denmark. Developing an effective control strategy requires knowledge of the epidemiology, as well as the genomic and virulent variability of the Danish A. salmonicida subsp. salmonicida isolates. To obtain this, the genomes of 101 A. salmonicida subsp. salmonicida, including 99 Danish isolates, one Scottish strain and the type strain NCIMB 1102, were sequenced using the Illumina HiSeq platform...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29245897/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#8
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29226517/natural-selection-beyond-genes-identification-and-analyses-of-evolutionarily-conserved-elements-in-the-genome-of-the-collared-flycatcher-ficedula-albicollis
#9
Rory J Craig, Alexander Suh, Mi Wang, Hans Ellegren
It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence is particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts...
December 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29220521/trypanosomatid-mitochondrial-rna-editing-dramatically-complex-transcript-repertoires-revealed-with-a-dedicated-mapping-tool
#10
Evgeny S Gerasimov, Anna A Gasparyan, Iosif Kaurov, Boris Tichý, Maria D Logacheva, Alexander A Kolesnikov, Julius Lukeš, Vyacheslav Yurchenko, Sara L Zimmer, Pavel Flegontov
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded...
December 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29219081/whole-genome-analysis-of-crispr-cas9-sgrna-off-target-homologies-via-an-efficient-computational-algorithm
#11
Hong Zhou, Michael Zhou, Daisy Li, Joseph Manthey, Ekaterina Lioutikova, Hong Wang, Xiao Zeng
BACKGROUND: The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. RESULTS: Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29216844/comparative-analyses-of-plastid-genomes-from-fourteen-cornales-species-inferences-for-phylogenetic-relationships-and-genome-evolution
#12
Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
BACKGROUND: The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. RESULTS: All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region...
December 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29209908/purification-and-characterization-of-exo-inulinase-from-paenibacillus-sp-d9-strain
#13
S Jeza, S B Maseko, J Lin
This study intended to purify and characterise exo-inulinase of diesel-degrading Paenibacillus sp. D9. The whole genome sequencing of Paenibacillus sp. D9 revealed to possess the sacC gene that is encoded as exo-inulinase/levanase. This isolate was capable of producing a maximum of 50.9 IU/mL of exo-inulinase activity within 3 days at 30 °C, 200 rpm and pH of 7.0 on minimal salt medium agar supplemented with 1% (w/v) inulin. An exo-inulinase of 58.5 kDa was purified using ammonium sulphate precipitation, HiTrap QFF column and MMC column chromatographies with a specific activity of 4333 IU/mg, 7...
December 5, 2017: Protein Journal
https://www.readbyqxmd.com/read/29206863/blood-collection-in-cell-stabilizing-tubes-does-not-impact-germline-dna-quality-for-pediatric-patients
#14
Bruce M Wollison, Edwin Thai, Aimee Mckinney, Abigail Ward, Andrea Clapp, Catherine Clinton, Anwesha Nag, Aaron R Thorner, Julie M Gastier-Foster, Brian D Crompton
OBJECTIVES: Liquid biopsy technologies allow non-invasive tumor profiling for patients with solid tumor malignancies by sequencing circulating tumor DNA. These studies may be useful in risk-stratification, monitoring for relapse, and understanding tumor evolution. The quality of DNA obtained for these studies is improved when blood samples are collected in tubes that stabilizing white blood cells (WBC). However, ongoing germline research in pediatric oncology generally requires obtaining blood samples in EDTA tubes, which do not contain a WBC-stabilizing preservative...
2017: PloS One
https://www.readbyqxmd.com/read/29206278/clinical-sequencing-from-raw-data-to-diagnosis-with-lifetime-value
#15
REVIEW
S M Caspar, N Dubacher, A M Kopps, J Meienberg, C Henggeler, G Matyas
High-throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step-by-step process from the generation of sequence data to molecular diagnosis of Mendelian diseases...
December 5, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29186799/whole-genome-re-alignment-facilitates-development-of-specific-molecular-markers-for-races-1-and-4-of-xanthomonas-campestris-pv-campestris-the-cause-of-black-rot-disease-in-brassica-oleracea
#16
(no author information available yet)
Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4 are the two most frequent races found in Brassica oleracea crops. In this study, a PCR molecular diagnostic tool was developed for the identification of Xcc races 1 and 4 of this pathogen. Whole genomic sequences of races 1, 3, 4 and 9 and sequences of three other Xanthomonas pathovars/species (X...
November 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29177972/conservation-of-the-enzyme-coenzyme-interfaces-in-fad-and-nadp-binding-adrenodoxin-reductase-a-ubiquitous-enzyme
#17
Israel Hanukoglu
FAD and NAD(P) together represent an ideal pair for coupled redox reactions in their capacity to accept two electrons and their redox potentials. Enzymes that bind both NAD(P) and FAD represent large superfamilies that fulfill essential roles in numerous metabolic pathways. Adrenodoxin reductase (AdxR) shares Rossmann fold features with some of these superfamilies but remains in a group of its own in the absence of sequence homology. This article documents the phylogenetic distribution of AdxR by examining whole genome databases for Metazoa, Plantae, Fungi, and Protista, and determines the conserved structural features of AdxR...
November 24, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29175309/altered-neuro-inflammatory-gene-expression-in-hippocampus-in-major-depressive-disorder
#18
Gouri J Mahajan, Eric J Vallender, Michael R Garrett, Lavanya Challagundla, James C Overholser, George Jurjus, Lesa Dieter, Maryam Syed, Damian G Romero, Hamed Benghuzzi, Craig A Stockmeier
Major Depressive Disorder (MDD) is a common psychiatric disorder for which available medications are often not effective. The high prevalence of MDD and modest response to existing therapies compels efforts to better understand and treat the disorder. Decreased hippocampal volume with increasing duration of depression suggests altered gene expression or even a decrease in neurogenesis. Tissue punches from the dentate gyrus were collected postmortem from 23 subjects with MDD and 23 psychiatrically-normal control subjects...
November 22, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29173093/molecular-network-selected-pharmacogenomics-in-a-case-of-bipolar-spectrum-disorder
#19
Stefano Fortinguerra, Alessandro Buriani, Vincenzo Sorrenti, Michele Lenzi, Pietro Giusti
Personal genomic analysis was used for molecular diagnosis and pharmacogenomics in a 53-year-old female suffering from alternating depressive and dysphoric episodes. A total of 52 genes and 108 SNPs were analyzed in the whole genome. Results from the pharmacogenomic analysis were consistent with the pharmacological history and indicate mutations associated with low monoaminergic tone, but also a hyperactive 5HT2A receptor, a feature that associates to a high probability of developing a bipolar condition, especially under 5-hydroxytryptamine potentiating pharmacology...
November 27, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/29171451/sequence-homology-and-expression-profile-of-genes-associated-with-dna-repair-pathways-in-mycobacterium-leprae
#20
Mukul Sharma, Sundeep Chaitanya Vedithi, Madhusmita Das, Anindya Roy, Mannam Ebenezer
BACKGROUND: Survival of Mycobacterium leprae, the causative bacteria for leprosy, in the human host is dependent to an extent on the ways in which its genome integrity is retained. DNA repair mechanisms protect bacterial DNA from damage induced by various stress factors. The current study is aimed at understanding the sequence and functional annotation of DNA repair genes in M. leprae. METHODS: T he genome of M. leprae was annotated using sequence alignment tools to identify DNA repair genes that have homologs in Mycobacterium tuberculosis and Escherichia coli...
October 2017: International Journal of Mycobacteriology
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