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Whole genome alignment

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https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#1
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...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28622346/flavivirus-and-filovirus-evoprinters-new-alignment-tools-for-the-comparative-analysis-of-viral-evolution
#2
Thomas Brody, Amarendra S Yavatkar, Dong Sun Park, Alexander Kuzin, Jermaine Ross, Ward F Odenwald
BACKGROUND: Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest...
June 16, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28612703/evolutionary-analysis-of-whole-genome-sequences-confirms-inter-farm-transmission-of-aleutian-mink-disease-virus
#3
Emma E Hagberg, Anders G Pedersen, Lars E Larsen, Anders Krarup
Aleutian mink disease virus (AMDV) is a frequently encountered pathogen associated with mink farming. Previous phylogenetic analyses of AMDV have been based on shorter and more conserved parts of the genome, e.g. the partial NS1 gene. Such fragments are suitable for detection but are less useful for elucidating transmission pathways while sequencing entire viral genomes provides additional informative sites and often results in better-resolved phylogenies. We explore how whole-genome sequencing can benefit investigations of AMDV transmission by reconstructing the relationships between AMDV field samples from a Danish outbreak...
June 13, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28589863/a-simple-and-economical-method-for-improving-whole-genome-alignment
#4
Huijun Mai, Tak-Wah Lam, Hing-Fung Ting
BACKGROUND: The recent advancement of whole genome alignment software has made it possible to align two genomes very efficiently and with only a small sacrifice in sensitivity. Yet it becomes very slow if the extra sensitivity is needed. This paper proposes a simple but effective method to improve the sensitivity of existing whole-genome alignment software without paying much extra running time. RESULTS AND CONCLUSIONS: We have applied our method to a popular whole genome alignment tool LAST, and we called the resulting tool LASTM...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28586236/inspecting-targeted-deep-sequencing-of-whole-genome-amplified-dna-versus-fresh-dna-for-somatic-mutation-detection-a-genetic-study-in-myelodysplastic-syndrome-patients
#5
Laura Palomo, Francisco Fuster-Tormo, Daniel Alvira, Vera Ademà, María Pilar Armengol, Paula Gómez-Marzo, Nuri de Haro, Mar Mallo, Blanca Xicoy, Lurdes Zamora, Francesc Solé
Whole genome amplification (WGA) has become an invaluable method for preserving limited samples of precious stock material and has been used during the past years as an alternative tool to increase the amount of DNA before library preparation for next-generation sequencing. Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic stem cell disorders characterized by presenting somatic mutations in several myeloid-related genes. In this work, targeted deep sequencing has been performed on four paired fresh DNA and WGA DNA samples from bone marrow of MDS patients, to assess the feasibility of using WGA DNA for detecting somatic mutations...
June 6, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28578460/genetic-variation-in-potential-giardia-vaccine-candidates-cyst-wall-protein-2-and-%C3%AE-1-giardin
#6
Matej Radunovic, Christian Klotz, Christina Skår Saghaug, Hans-Richard Brattbakk, Toni Aebischer, Nina Langeland, Kurt Hanevik
Giardia is a prevalent intestinal parasitic infection. The trophozoite structural protein a1-giardin (a1-g) and the cyst protein cyst wall protein 2 (CWP2) have shown promise as Giardia vaccine antigen candidates in murine models. The present study assesses the genetic diversity of a1-g and CWP2 between and within assemblages A and B in human clinical isolates. a1-g and CWP2 sequences were acquired from 15 Norwegian isolates by PCR amplification and 20 sequences from German cultured isolates by whole genome sequencing...
June 3, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28578134/investigation-of-copy-number-variation-in-subjects-with-major-depression-based-on-whole-genome-sequencing-data
#7
Chenglong Yu, Bernhard T Baune, Ma-Li Wong, Julio Licinio
BACKGROUND: Despite recent intensive research using genome-wide association studies, the underlying biological basis of major depressive disorder (MDD) still remains unknown. In contrast to genotyping platforms which identify specific variations, whole-genome sequencing (WGS) allows us to detect all private genetic variations within an individual. So far there have been no studies investigating copy number variations (CNVs) in subjects with MDD using WGS data. METHODS: We obtained complete WGS paired-end reads data of 15 MDD patients and 10 ethnically matched healthy controls...
May 30, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28576740/draft-genome-sequence-of-a-kluyvera-intermedia-isolate-from-a-patient-with-a-pancreatic-abscess
#8
Roland Thele, Heidi Gumpert, Louise B Christensen, Peder Worning, Kristian Schønning, Henrik Westh, Thomas A Hansen
The genus Kluyvera comprises potential pathogens that can cause many infections. This study reports a Kluyvera intermedia strain (FOSA7093) from a pancreatic cyst specimen from a long-term hospitalised patient. Whole-genome sequencing (WGS) of the K. intermedia isolate was performed and the strain was reported as sensitive to Danish-registered antibiotics although it had a fosA-like gene in the genome. There were nine contigs that aligned to a plasmid, and these contigs contained several heavy metal resistance gene homologues...
May 30, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28570142/an-efficient-approach-to-explore-and-discriminate-anomalous-regions-in-bacterial-genomes-based-on-maximum-entropy
#9
Gesiele Almeida Barros-Carvalho, Marie-Anne Van Sluys, Fabricio Martins Lopes
Recently, there has been an increase in the number of whole bacterial genomes sequenced, mainly due to the advancing of next-generation sequencing technologies. In face of this, there is a need to provide new analytical alternatives that can follow this advance. Given our current knowledge about the genomic plasticity of bacteria and that those genomic regions can uncover important features about this microorganism, our goal was to develop a fast methodology based on maximum entropy (ME) to guide the researcher to regions that could be prioritized during the analysis...
June 1, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28541377/asap-a-web-based-platform-for-the-analysis-and-interactive-visualization-of-single-cell-rna-seq-data
#10
Vincent Gardeux, Fabrice P A David, Adrian Shajkofci, Petra C Schwalie, Bart Deplancke
Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet these groups often lack the expertise to handle complex scRNA-seq data sets. Results: We developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28539120/comprehensive-whole-genome-sequence-analyses-yields-novel-genetic-and-structural-insights-for-intellectual-disability
#11
Farah R Zahir, Jill C Mwenifumbo, Hye-Jung E Chun, Emilia L Lim, Clara D M Van Karnebeek, Madeline Couse, Karen L Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F Boerkoel, Sylvie L Langlois, Barbara M McGillivray, Steven J M Jones, Jan M Friedman, Marco A Marra
BACKGROUND: Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS: We conducted WGS on eight children with idiopathic ID and brain structural defects, and their normal parents; carrying out an extensive data analyses, using standard and discovery approaches...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28525288/inference-of-the-genetic-polymorphisms-of-cyp2d6-in-six-subtribes-of-the-malaysian-orang-asli-from-whole-genome-sequencing-data
#12
Choo Yee Yu, Geik Yong Ang, Vinothini Subramaniam, Richard Johari James, Aminuddin Ahmad, Thuhairah Abdul Rahman, Fadzilah Mohd Nor, Syahrul Azlin Shaari, Lay Kek Teh, Mohd Zaki Salleh
AIMS: CYP2D6 is one of the major enzymes in the cytochrome P450 monooxygenase system. It metabolizes ∼25% of prescribed drugs and hence, the genetic diversity of CYP2D6 gene has continued to be of great interest to the medical and pharmaceutical industries. This study aims to perform a systematic analysis of the CYP2D6 gene in six subtribes of the Malaysian Orang Asli. METHODS: Genomic DNAs were extracted from the blood samples followed by whole-genome sequencing...
May 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28511677/a-strategy-to-improve-phasing-of-whole-genome-sequenced-individuals-through-integration-of-familial-information-from-dense-genotype-panels
#13
Pierre Faux, Tom Druet
BACKGROUND: Haplotype reconstruction (phasing) is an essential step in many applications, including imputation and genomic selection. The best phasing methods rely on both familial and linkage disequilibrium (LD) information. With whole-genome sequence (WGS) data, relatively small samples of reference individuals are generally sequenced due to prohibitive sequencing costs, thus only a limited amount of familial information is available. However, reference individuals have many relatives that have been genotyped (at lower density)...
May 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#14
Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28492527/single-cell-template-strand-sequencing-by-strand-seq-enables-the-characterization-of-individual-homologs
#15
Ashley D Sanders, Ester Falconer, Mark Hills, Diana C J Spierings, Peter M Lansdorp
The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange events and exploring cellular heterogeneity. Strand-seq is a single-cell sequencing technology that resolves the individual homologs within a cell by restricting sequence analysis to the DNA template strands used during DNA replication...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28486572/evaluation-of-mc1r-high-throughput-nucleotide-sequencing-data-generated-by-the-1000-genomes-project
#16
Leonardo Arduino Marano, Letícia Marcorin, Erick da Cruz Castelli, Celso Teixeira Mendes-Junior
The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology...
May 8, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28481935/genotypic-and-phenotypic-characterization-of-multidrug-resistant-salmonella-typhimurium-and-salmonella-kentucky-strains-recovered-from-chicken-carcasses
#17
Rizwana Tasmin, Nur A Hasan, Christopher J Grim, Ar'Quette Grant, Seon Young Choi, M Samiul Alam, Rebecca Bell, Christopher Cavanaugh, Kannan V Balan, Uma S Babu, Salina Parveen
Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28473773/analyses-of-mmp20-missense-mutations-in-two-families-with-hypomaturation-amelogenesis-imperfecta
#18
Youn Jung Kim, Jenny Kang, Figen Seymen, Mine Koruyucu, Koray Gencay, Teo Jeon Shin, Hong-Keun Hyun, Zang Hee Lee, Jan C-C Hu, James P Simmer, Jung-Wook Kim
Amelogenesis imperfecta is a group of rare inherited disorders that affect tooth enamel formation, quantitatively and/or qualitatively. The aim of this study was to identify the genetic etiologies of two families presenting with hypomaturation amelogenesis imperfecta. DNA was isolated from peripheral blood samples obtained from participating family members. Whole exome sequencing was performed using DNA samples from the two probands. Sequencing data was aligned to the NCBI human reference genome (NCBI build 37...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28453674/ntcard-a-streaming-algorithm-for-cardinality-estimation-in-genomics-data
#19
Hamid Mohamadi, Hamza Khan, Inanc Birol
Motivation: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k -mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k -mers, or even better, to build a histogram of k -mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449639/clovr-comparative-automated-cloud-enabled-comparative-microbial-genome-sequence-analysis-pipeline
#20
Sonia Agrawal, Cesar Arze, Ricky S Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M Fraser, Hervé Tettelin, Owen White, Samuel V Angiuoli, Anup Mahurkar, W Florian Fricke
BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. RESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI...
April 27, 2017: BMC Genomics
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