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https://www.readbyqxmd.com/read/28528020/optimal-hybrid-sequencing-and-assembly-feasibility-conditions-for-accurate-genome-reconstruction-and-cost-minimization-strategy
#1
Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, Byung-Jun Yoon
Recent advances in high-throughput genome sequencing technologies have enabled the systematic study of various genomes by making whole genome sequencing affordable. Modern sequencers generate a huge number of small sequence fragments called reads, where the read length and the per-base sequencing cost depend on the technology used. To date, many hybrid genome assembly algorithms have been developed that can take reads from multiple read sources to reconstruct the original genome. However, rigorous investigation of the feasibility conditions for complete genome reconstruction and the optimal sequencing strategy for minimizing the sequencing cost has been conspicuously missing...
April 3, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28526730/a-targeted-capture-linkage-map-anchors-the-genome-of-the-schistosomiasis-vector-snail-biomphalaria-glabrata
#2
Jacob A Tennessen, Stephanie R Bollmann, Michael S Blouin
The aquatic planorbid snail Biomphalaria glabrate is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here we used targeted capture markers to map over 10,000 B. glabrate scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups. We added additional scaffolds to these linkage groups based on linkage disequilibrium analysis of targeted capture and whole-genome sequences of 96 unrelated snails...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#3
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
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
#4
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/28523015/transcription-factors-in-fungi-tfome-dynamics-three-major-families-and-dual-specificity-tfs
#5
Ekaterina Shelest
Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28522810/integrative-analysis-of-genomic-sequencing-data-reveals-higher-prevalence-of-lrp1b-mutations-in-lung-adenocarcinoma-patients-with-copd
#6
Dakai Xiao, Fuqiang Li, Hui Pan, Han Liang, Kui Wu, Jianxing He
Both chronic Obstruction Pulmonary Disease (COPD) and lung cancer are leading causes of death globally. Although COPD and lung cancer coexist frequently, it is unknown whether lung cancer patients with COPD harbor distinct genomic characteristics compared to those without COPD. In this study, we retrospectively analyzed genomic sequencing data from 272 patients with lung adenocarcinoma (LUAD) and compared the genetic alterations in LUAD patients with and without COPD. Integrative analysis of whole-genome and exome sequencing data revealed that COPD and non-COPD groups showed high concordance in mutational burden and spectra...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#7
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#8
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28521875/exome-sequencing-reveals-a-de-novo-pold1-mutation-causing-phenotypic-variability-in-mandibular-hypoplasia-deafness-progeroid-features-and-lipodystrophy-syndrome-mdpl
#9
Sahar Elouej, Ana Beleza-Meireles, Richard Caswell, Kevin Colclough, Sian Ellard, Jean Pierre Desvignes, Christophe Béroud, Nicolas Lévy, Shehla Mohammed, Annachiara De Sandre-Giovannoli
BACKGROUND: Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL) is an autosomal dominant systemic disorder characterized by prominent loss of subcutaneous fat, a characteristic facial appearance and metabolic abnormalities. This syndrome is caused by heterozygous de novo mutations in the POLD1 gene. To date, 19 patients with MDPL have been reported in the literature and among them 14 patients have been characterized at the molecular level. Twelve unrelated patients carried a recurrent in-frame deletion of a single codon (p...
June 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#10
Kelin Xu, Li Jin, Momiao Xiong
BACKGROUND: Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521728/a-method-for-the-allocation-of-sequencing-resources-in-genotyped-livestock-populations
#11
Serap Gonen, Roger Ros-Freixedes, Mara Battagin, Gregor Gorjanc, John M Hickey
BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level...
May 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28521008/gemstone-orchestrated-prioritization-of-human-germline-mutations-in-the-cloud
#12
Siwei Chen, Juan F Beltrán, Clara Esteban-Jurado, Sebastià Franch-Expósito, Sergi Castellví-Bel, Steven Lipkin, Xiaomu Wei, Haiyuan Yu
Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28521002/changes-in-microbiome-during-and-after-travellers-diarrhea-what-we-know-and-what-we-do-not
#13
David A Rasko
The study of bacterial pathogens has advanced from culture on plates to basic biochemical studies; to sequencing reference genomes and attempting to ascribe those qualities to the whole species; to evaluating complete communities based on the universal marker of the 16S rRNA gene; to now sequencing all available nucleic acids in any sample to characterize the community as a whole. These types of scientific advances highlight that there are multiple layers of information within any sample, and to some extent we are only now beginning to be able to identify, categorize and understand the complex interactions of the host, pathogen and microbiome...
April 1, 2017: Journal of Travel Medicine
https://www.readbyqxmd.com/read/28520856/control-of-multidrug-resistant-pseudomonas-aeruginosa-in-allogeneic-hematopoietic-stem-cell-transplant-recipients-by-a-novel-bundle-including-remodeling-of-sanitary-and-water-supply-systems
#14
A Kossow, S Kampmeier, S Willems, W E Berdel, A H Groll, B Burckhardt, Rossig C, C Groth, E A Idelevich, F Kipp, A Mellmann, M Stelljes
Background.: Infections by multidrug-resistant Pseudomonas aeruginosa (MDRPa) are an important cause of morbidity and mortality in patients after allogeneic hematopoietic stem cell transplantation (HSCT). Humid environments can serve as a reservoir and source of infection by this pathogen. To minimize the risk of infection from these reservoirs, we performed extensive remodeling of sanitation and water installations as the focus of our hygiene bundle. Methods.: During the reconstruction of our transplantation unit (April 2011- April 2014) we implemented several technical modifications to reduce environmental contamination by and subsequent spreading of MDRPa, including a newly designed shower drain, disinfecting siphons underneath the sinks, and rimless toilets...
May 18, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28518168/using-high-resolution-variant-frequencies-to-empower-clinical-genome-interpretation
#15
Nicola Whiffin, Eric Minikel, Roddy Walsh, Anne H O'Donnell-Luria, Konrad Karczewski, Alexander Y Ing, Paul J R Barton, Birgit Funke, Stuart A Cook, Daniel MacArthur, James S Ware
PurposeWhole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28518029/influenza-a-h9n2-virus-myanmar-2014-2015
#16
Thant Nyi Lin, Nutthawan Nonthabenjawan, Supassama Chaiyawong, Napawan Bunpapong, Supanat Boonyapisitsopa, Taveesak Janetanakit, Pont Pont Mon, Hla Hla Mon, Kyaw Naing Oo, Sandi Myint Oo, Mar Mar Win, Alongkorn Amonsin
Routine surveillance of influenza A virus was conducted in Myanmar during 2014-2015. Influenza A(H9N2) virus was isolated in Shan State, upper Myanmar. Whole-genome sequencing showed that H9N2 virus from Myanmar was closely related to H9N2 virus of clade 4.2.5 from China.
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28516866/invasive-serotype-35b-pneumococci-including-an-expanding-serotype-switch-lineage-united-states-2015-2016
#17
Sopio Chochua, Benjamin J Metcalf, Zhongya Li, Hollis Walker, Theresa Tran, Lesley McGee, Bernard Beall
We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015-2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post-pneumococcal 7-valent conjugate vaccine years (2001-2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28516864/genomic-analysis-of-salmonella-enterica-serovar-typhimurium-dt160-associated-with-a-14-year-outbreak-new-zealand-1998-2012
#18
Samuel J Bloomfield, Jackie Benschop, Patrick J Biggs, Jonathan C Marshall, David T S Hayman, Philip E Carter, Anne C Midwinter, Alison E Mather, Nigel P French
During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28516087/dna-sequence-analysis-in-clinical-medicine-proceeding-cautiously
#19
REVIEW
Moyra Smith
Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28516035/dna-shotgun-sequencing-analysis-of-garcinia-mangostana-l-variety-mesta
#20
Syuhaidah Abu Bakar, Suresh Kumar, Kok-Keong Loke, Hoe-Han Goh, Normah Mohd Noor
Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark purple fruits with white flesh. The xanthone-rich purple pericarp tissue contains valuable compounds with medicinal properties. Following previously reported genome sequencing of a common variety of mangosteen [1], we performed another whole genome sequencing of a commercially popular variety of this fruit species (var. Mesta) for comparative analysis of its genome composition. Raw reads of the DNA sequencing project were deposited to SRA database with the accession number SRX2709728...
June 2017: Genomics Data
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