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Human whole genome sequencing

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https://www.readbyqxmd.com/read/29331684/reprogramming-neurodegeneration-in-the-big-data-era
#1
REVIEW
Lujia Zhou, Patrik Verstreken
Recent genome-wide association studies (GWAS) have identified numerous genetic risk variants for late-onset Alzheimer's disease (AD) and Parkinson's disease (PD). However, deciphering the functional consequences of GWAS data is challenging due to a lack of reliable model systems to study the genetic variants that are often of low penetrance and non-coding identities. Pluripotent stem cell (PSC) technologies offer unprecedented opportunities for molecular phenotyping of GWAS variants in human neurons and microglia...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29331671/the-molecular-characteristics-of-avian-influenza-viruses-h9n2-derived-from-air-samples-in-live-poultry-markets
#2
Yanheng Wu, Jinsi Lin, Shuhuan Yang, Ying Xie, Man Wang, Xueqin Chen, Yayang Zhu, Le Luo, Wuyang Shi
OBJECTIVE: To study the molecular characteristics of H9N2-subtype avian influenza viruses (AIVs) isolated from air samples collected in live poultry markets (LPMs) and explore their sequence identities with AIVs that caused human infection. METHODS: Weekly surveillance of H9N2-subtype AIVs in the air of LPMs was conducted from 2015 to 2016. H9-positive samples were isolated from chicken embryos. Whole genome sequences of the isolated AIVs were obtained through high-throughput sequencing...
January 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29330370/a-rna-sequencing-approach-for-the-identification-of-novel-long-non-coding-rna-biomarkers-in-colorectal-cancer
#3
Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C Richard Boland, Ajay Goel
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29326229/genomic-understanding-of-an-infectious-brain-disease-from-the-desert
#4
Leandro F Moreno, Abdalla A O Ahmed, Balázs Brankovics, Christina A Cuomo, Steph B J Menken, Saad J Taj-Aldeen, Hani Faidah, J Benjamin Stielow, Marcus de M Teixeira, Francesc X Prenafeta-Boldú, Vania A Vicente, Sybren de Hoog
Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper we describe the whole genome re-sequencing of two Rhinocladiella mackenziei strains from patients in Saudi Arabia and Qatar...
January 11, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29325576/reanalysis-of-chinese-treponema-pallidum-samples-all-chinese-samples-cluster-with-ss14-like-group-of-syphilis-causing-treponemes
#5
Michal Strouhal, Jan Oppelt, Lenka Mikalová, Natasha Arora, Kay Nieselt, Fernando González-Candelas, David Šmajs
OBJECTIVE: Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget...
January 11, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29324680/phylogenetic-analysis-and-characterization-of-a-sporadic-isolate-of-equine-influenza-a-h3n8-from-an-unvaccinated-horse-in-2015
#6
Chithra C Sreenivasan, Sunayana S Jandhyala, Sisi Luo, Ben M Hause, Milton Thomas, David E B Knudsen, Pamela Leslie-Steen, Travis Clement, Stephanie E Reedy, Thomas M Chambers, Jane Christopher-Hennings, Eric Nelson, Dan Wang, Radhey S Kaushik, Feng Li
Equine influenza, caused by the H3N8 subtype, is a highly contagious respiratory disease affecting equid populations worldwide and has led to serious epidemics and transboundary pandemics. This study describes the phylogenetic characterization and replication kinetics of recently-isolated H3N8 virus from a nasal swab obtained from a sporadic case of natural infection in an unvaccinated horse from Montana, USA. The nasal swab tested positive for equine influenza by Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR)...
January 11, 2018: Viruses
https://www.readbyqxmd.com/read/29321570/transfer-of-a-bla-ctx-m-1-carrying-plasmid-between-different-escherichia-coli-strains-within-the-human-gut-explored-by-whole-genome-sequencing-analyses
#7
Per Kristian Knudsen, Karianne Wiger Gammelsrud, Kristian Alfsnes, Martin Steinbakk, Tore G Abrahamsen, Fredrik Müller, Jon Bohlin
Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven bla CTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320538/germline-and-somatic-variant-identification-using-bgiseq-500-and-hiseq-x-ten-whole-genome-sequencing
#8
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/29317534/linking-secondary-metabolites-to-gene-clusters-through-genome-sequencing-of-six-diverse-aspergillus-species
#9
Inge Kjærbølling, Tammi C Vesth, Jens C Frisvad, Jane L Nybo, Sebastian Theobald, Alan Kuo, Paul Bowyer, Yudai Matsuda, Stephen Mondo, Ellen K Lyhne, Martin E Kogle, Alicia Clum, Anna Lipzen, Asaf Salamov, Chew Yee Ngan, Chris Daum, Jennifer Chiniquy, Kerrie Barry, Kurt LaButti, Sajeet Haridas, Blake A Simmons, Jon K Magnuson, Uffe H Mortensen, Thomas O Larsen, Igor V Grigoriev, Scott E Baker, Mikael R Andersen
The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation...
January 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29317018/outbreak-of-salmonella-bovismorbificans-associated-with-the-consumption-of-uncooked-ham-products-the-netherlands-2016-to-2017
#10
Diederik Brandwagt, Cees van den Wijngaard, Anna Dolores Tulen, Annemieke Christine Mulder, Agnetha Hofhuis, Rianne Jacobs, Max Heck, Anjo Verbruggen, Hans van den Kerkhof, Ife Slegers-Fitz-James, Lapo Mughini-Gras, Eelco Franz
In January 2017, an increase in reported Salmonellaenterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54 S...
January 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29310579/gene-trait-matching-across-the-bifidobacterium-longum-pan-genome-reveals-considerable-diversity-in-carbohydrate-catabolism-among-human-infant-strains
#11
Silvia Arboleya, Francesca Bottacini, Mary O'Connell-Motherway, C Anthony Ryan, R Paul Ross, Douwe van Sinderen, Catherine Stanton
BACKGROUND: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B...
January 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29306352/porcine-commensal-escherichia-coli-a-reservoir-for-class-1-integrons-associated-with-is26
#12
Cameron J Reid, Ethan R Wyrsch, Piklu Roy Chowdhury, Tiziana Zingali, Michael Liu, Aaron E Darling, Toni A Chapman, Steven P Djordjevic
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia...
December 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29304755/computational-approach-to-discriminate-human-and-mouse-sequences-in-patient-derived-tumour-xenografts
#13
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/29301233/analyses-of-tissue-culture-adaptation-of-human-herpesvirus-6a-by-whole-genome-deep-sequencing-redefines-the-reference-sequence-and-identifies-virus-entry-complex-changes
#14
Joshua G Tweedy, Eric Escriva, Maya Topf, Ursula A Gompels
Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus entry complex, which affected cellular tropism, virulence, and vaccine development. Here, we analyse these effects on the reference genome for related betaherpesviruses, Roseolovirus, human herpesvirus 6A (HHV-6A) strain U1102. This virus is also naturally "cloned" by germline subtelomeric chromosomal-integration in approximately 1% of human populations, and accurate references are key to understanding pathological relationships between exogenous and endogenous virus...
December 31, 2017: Viruses
https://www.readbyqxmd.com/read/29298123/molecular-characterization-of-pseudomonas-putida-group-isolates-carrying-blavim-2-disseminated-in-a-university-hospital-in-korea
#15
Jun Sung Hong, Eun-Jeong Yoon, Wonkeun Song, Yu Bin Seo, Saeam Shin, Min-Jeong Park, Seok Hoon Jeong, Kyungwon Lee
Pseudomonas putida group are Gram-negative bacilli with polar flagellation, which are ubiquitous in the environment, although they are rarely involved in human infections. The aim of this study was to identify the dissemination of VIM-2-producing P. putida group in clinical isolates from a hospital in Korea. Thirteen strains were collected from 2014 to 2015 for the study. The isolates were recovered from urine cultures of both inpatients and outpatients at the hospital. Minimum inhibitory concentrations of antibiotics were determined by Etest...
January 3, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29297313/a-compendium-and-functional-characterization-of-mammalian-genes-involved-in-adaptation-to-arctic-or-antarctic-environments
#16
Nikolay S Yudin, Denis M Larkin, Elena V Ignatieva
BACKGROUND: Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29290336/genome-wide-study-of-atrial-fibrillation-identifies-seven-risk-loci-and-highlights-biological-pathways-and-regulatory-elements-involved-in-cardiac-development
#17
Jonas B Nielsen, Lars G Fritsche, Wei Zhou, Tanya M Teslovich, Oddgeir L Holmen, Stefan Gustafsson, Maiken E Gabrielsen, Ellen M Schmidt, Robin Beaumont, Brooke N Wolford, Maoxuan Lin, Chad M Brummett, Michael H Preuss, Lena Refsgaard, Erwin P Bottinger, Sarah E Graham, Ida Surakka, Yunhan Chu, Anne Heidi Skogholt, Håvard Dalen, Alan P Boyle, Hakan Oral, Todd J Herron, Jacob Kitzman, José Jalife, Jesper H Svendsen, Morten S Olesen, Inger Njølstad, Maja-Lisa Løchen, Aris Baras, Omri Gottesman, Anthony Marcketta, Colm O'Dushlaine, Marylyn D Ritchie, Tom Wilsgaard, Ruth J F Loos, Timothy M Frayling, Michael Boehnke, Erik Ingelsson, David J Carey, Frederick E Dewey, Hyun M Kang, Gonçalo R Abecasis, Kristian Hveem, Cristen J Willer
Atrial fibrillation (AF) is a common cardiac arrhythmia and a major risk factor for stroke, heart failure, and premature death. The pathogenesis of AF remains poorly understood, which contributes to the current lack of highly effective treatments. To understand the genetic variation and biology underlying AF, we undertook a genome-wide association study (GWAS) of 6,337 AF individuals and 61,607 AF-free individuals from Norway, including replication in an additional 30,679 AF individuals and 278,895 AF-free individuals...
December 27, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29289333/understanding-neurodevelopmental-disorders-the-promise-of-regulatory-variation-in-the-3-utrome
#18
REVIEW
Kai A Wanke, Paolo Devanna, Sonja C Vernes
Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders...
November 14, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29286447/simultaneous-mapping-and-quantitation-of-ribonucleotides-in-human-mitochondrial-dna
#19
Katrin Kreisel, Martin K M Engqvist, Anders R Clausen
Established approaches to estimate the number of ribonucleotides present in a genome are limited to the quantitation of incorporated ribonucleotides using short synthetic DNA fragments or plasmids as templates and then extrapolating the results to the whole genome. Alternatively, the number of ribonucleotides present in a genome may be estimated using alkaline gels or Southern blots. More recent in vivo approaches employ Next-generation sequencing allowing genome-wide mapping of ribonucleotides, providing the position and identity of embedded ribonucleotides...
November 14, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29285825/targeted-copy-number-screening-highlights-an-intragenic-deletion-of-wdr63-as-the-likely-cause-of-human-occipital-encephalocele-and-abnormal-cns-development-in-zebrafish
#20
Wolfgang Hofmeister, Maria Pettersson, Deniz Kurtoglu, Miriam Armenio, Jesper Eisfeldt, Nikos Papadogiannakis, Peter Gustavsson, Anna Lindstrand
Congenital malformations affecting the neural tube can present as isolated malformations or occur in association with other developmental abnormalities and syndromes. Using high resolution copy number screening in 66 fetuses with neural tube defects we identified 6 fetuses with likely pathogenic mutations, three aneuploidies (one trisomy 13 and two trisomy 18) and three deletions previously reported in NTDs (one 22q11.2 deletion and two 1p36 deletions) corresponding to 9% of the cohort. In addition, we identified five rare deletions and two duplications of uncertain significance including a rare intragenic heterozygous in-frame WDR63 deletion in a fetus with occipital encephalocele...
December 28, 2017: Human Mutation
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