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https://www.readbyqxmd.com/read/28749196/double-stranded-telomeric-dna-binding-proteins-diversity-matters
#1
Filip Červenák, Katarína Juríková, Regina Sepšiová, Martina Neboháčová, Jozef Nosek, Ľubomír Tomáška
Telomeric sequences constitute only a small fraction of the whole genome yet they are crucial for ensuring genomic stability. This function is in large part mediated by protein complexes recruited to telomeric sequences by specific telomere-binding proteins (TBPs). Although the principal tasks of nuclear telomeres are the same in all eukaryotes, TBPs in various taxa exhibit a surprising diversity indicating their distinct evolutionary origin. This diversity is especially pronounced in ascomycetous yeasts where they must have co-evolved with rapidly diversifying sequences of telomeric repeats...
July 27, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28748527/the-prevalence-of-dicer1-pathogenic-variation-in-population-databases
#2
Jung Kim, Amanda Field, Kris Ann P Schultz, D Ashley Hill, Douglas R Stewart
The DICER1 syndrome is associated with a variety of rare benign and malignant tumors, including pleuropulmonary blastoma (PPB), cystic nephroma (CN) and Sertoli-Leydig cell tumor (SLCT). The prevalence and penetrance of pathogenic DICER1 variation in the general population is unknown. We examined three publicly-available germline whole exome sequence datasets: Exome Aggregation Consortium (ExAC), 1000 Genomes (1000G), and the Exome Sequencing Project (ESP). To avoid over-estimation of pathogenic DICER1 variation from cancer-associated exomes, we excluded The Cancer Genome Atlas (TCGA) variants from ExAC...
July 27, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28748134/genomic-characterization-reconfirms-the-taxonomic-status-of-lactobacillus-parakefiri
#3
Yasuhiro Tanizawa, Hisami Kobayashi, Eli Kaminuma, Mitsuo Sakamoto, Moriya Ohkuma, Yasukazu Nakamura, Masanori Arita, Masanori Tohno
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573(T) to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L...
2017: Bioscience of Microbiota, Food and Health
https://www.readbyqxmd.com/read/28747754/corrigendum-whole-genome-sequencing-identifies-rare-genotypes-in-comp-and-chadl-associated-with-high-risk-of-hip-osteoarthritis
#4
Unnur Styrkarsdottir, Hannes Helgason, Asgeir Sigurdsson, Gudmundur L Norddahl, Arna B Agustsdottir, Louise N Reynard, Amanda Villalvilla, Gisli H Halldorsson, Aslaug Jonasdottir, Audur Magnusdottir, Asmundur Oddson, Gerald Sulem, Florian Zink, Gardar Sveinbjornsson, Agnar Helgason, Hrefna S Johannsdottir, Anna Helgadottir, Hreinn Stefansson, Solveig Gretarsdottir, Thorunn Rafnar, Ina S Almdahl, Anne Brækhus, Tormod Fladby, Geir Selbæk, Farhad Hosseinpanah, Fereidoun Azizi, Jung Min Koh, Nelson L S Tang, Maryams Danesphour, Jose I Mayordomo, Corrine Welt, Peter S Braund, Nilesh J Samani, Lambertus A Kiemeney, L Stefan Lohmander, Claus Christiansen, Ole A Andreassen, arcOGEN Consortium, Olafur Magnusson, Gisli Masson, Augustine Kong, Ingileif Jonsdottir, Daniel Gudbjartsson, Patrick Sulem, Helgi Jonsson, John Loughlin, Thorvaldur Ingvarsson, Unnur Thorsteinsdottir, Kari Stefansson
No abstract text is available yet for this article.
July 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28747504/targeted-genome-sequencing-reveals-varicella-zoster-virus-open-reading-frame-12-deletion
#5
Randall J Cohrs, Katherine S Lee, Addilynn Beach, Bridget Sanford, Nicholas L Baird, Christina Como, Chiharu Graybill, Dallas Jones, Eden Tekeste, Mitchell Ballard, Xiaomi Chen, David Yalacki, Seth Frietze, Kenneth Jones, Tihana Lenac Rovis, Stipan Jonjić, Jürgen Haas, Don Gilden
The neurotropic herpesvirus varicella zoster virus (VZV) establishes a life-long latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernable growth defect in tissue culture, contained a 2158-bp deletion in open reading frame (ORF) 12...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28747373/investigation-of-respiratory-syncytial-virus-outbreak-on-an-adult-stem-cell-transplant-unit-using-whole-genome-sequencing
#6
Yijun Zhu, Teresa R Zembower, Kristen E Metzger, Zhengdeng Lei, Stefan J Green, Chao Qi
A viral whole genome sequencing strategy, based on PCR amplification followed by Next-generation Sequencing, was used to investigate a nosocomial RSV-B outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and healthcare workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs with an identical RSV-B strain which were clearly distinct from strains recovered from individuals unrelated to the outbreak...
July 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28747224/regions-of-common-inter-individual-dna-methylation-differences-in-human-monocytes-genetic-basis-and-potential-function
#7
Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
BACKGROUND: There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. RESULTS: We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before...
July 26, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28746838/whole-genome-characterization-of-a-novel-porcine-reproductive-and-respiratory-syndrome-virus-1-isolate-genetic-evidence-for-recombination-between-amervac-vaccine-and-circulating-strains-in-mainland-china
#8
Nanhua Chen, Qiaorong Liu, Mingming Qiao, Xiaoyu Deng, Xizhao Chen, Ming Sun
Genotype 1 porcine reproductive and respiratory syndrome virus (PRRSV 1) have been continuously isolated in China in recent years. Complete genome sequences of these isolates are important to investigate the prevalence and evolution of Chinese PRRSV 1. Herein, we describe the isolation of a novel PRRSV 1 isolate, denominated HLJB1, in the Heilongjiang province of China. Complete genome sequencing of HLJB1 showed that it shares 90.66% and 58.21% nucleotide identities with PRRSV 1 and 2 prototypic strains Lelystad virus and ATCC VR-2332, respectively...
July 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28746784/whole-genome-sequencing-approaches-for-conservation-biology-advantages-limitations-and-practical-recommendations
#9
Angela P Fuentes-Pardo, Daniel E Ruzzante
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq), and the sequencing of multiple individuals from a population to a low depth (lcWGR)...
July 26, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28746207/integrating-nested-pcr-with-high-throughput-sequencing-to-characterize-mutations-of-hbv-genome-in-low-viral-load-samples
#10
Xianjun Wang, Lihui Xu, Yueming Chen, Anbing Liu, Liqian Wang, Peisong Xu, Yunhui Liu, Lei Li, Fei Meng
Due to the low viral load of hepatitis B virus (HBV) in plasma samples, conventional techniques have limitations to the detection of antiviral resistance mutations. To solve the problem, we developed a fast, highly sensitive, and accurate method to sequence the HBV whole-genome sequencing in plasma samples which had various viral loads from very low to high.Twenty-one plasma samples were collected from patients who were carriers of HBV from the Hangzhou First People's Hospital. Two pairs of conserved, overlapping, nested primers were used to amplify and sequence the whole HBV genome in 8 plasma samples with different viral loads...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28746191/whole-exome-sequencing-unveils-a-frameshift-mutation-in-cngb3-for-cone-dystrophy-a-case-report-of-an-indian-family
#11
Shashank Gupta, Amit Chaurasia, Ekta Pathak, Rajeev Mishra, Vidya Nair Chaudhry, Prashaant Chaudhry, Ashim Mukherjee, Mousumi Mutsuddi
RATIONALE: Genetic elucidation of cone-dominated retinal dystrophies in Indian subcontinent is much needed to identify and catalog underlying genetic defects. In this context, the present study recruited a consanguineous Indian family affected with autosomal recessive cone dystrophy (CD). Considering the huge genetic heterogeneity and recessive inheritance of the disease, we chose to dissect out causal variant in this family by whole exome sequencing (WES). PATIENT CONCERNS: In the recruited family, three of the six siblings had complaints of poor visual acuity, photophobia, and disturbed colour vision since early childhood...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28745674/-gene-mutations-in-patients-with-hereditary-cavernous-malformations
#12
O B Belousova, E S Bulygina, D N Okishev, E B Prohorchuk, S V Tsygankova, I N Pronin, L V Shishkina, M V Ryzhova, K G Skryabin, A N Konovalov
AIM: To identify mutations in cerebral cavernous malformation (CCM) genes in patients with hereditary and sporadic CCMs in the Russian population. MATERIAL AND METHODS: Blood samples from 73 randomly selected patients, including 29 MRI-confirmed familial cases, 8 clinically confirmed familial cases and 38 so-called sporadic cases, were examined. A search for large deletions/duplications was performed using multiplex ligation-dependent probe amplification (MPLA)...
2017: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/28743649/first-report-of-blaoxa-181-mediated-carbapenem-resistance-in-aeromonas-caviae-in-association-with-pkp3-a-threat-for-rapid-dissemination
#13
Shalini Anandan, Radha Gopi, Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi Sethuvel, Priya Gunasekaran, Kamini Walia, Balaji Veeraraghavan
OBJECTIVES: Aeromonas spp producing carbapenemases is of great concern in health-care settings and also known to acquire clinically relevant resistance genes. In this study, carbapenem non-susceptible Aeromonas isolates were characterized for their molecular mechanism. METHOD: Out of 180 Aeromonas isolates, 10 carbapenem non-susceptible isolates were selected based on their antimicrobial susceptibility profile. Carbapenemase production was investigated using CarbaNP method...
July 22, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28743260/molecular-evolution-of-two-asymptomatic-echovirus-6-strains-that-constitute-a-novel-branch-of-recently-epidemic-echovirus-6-in-china
#14
Hao Sun, Xiaoqin Huang, Keqin Lin, Kai Huang, Jiayou Chu, Zhaoqing Yang, Shaohui Ma
BACKGROUND: Echovirus 6 (E6) infections are associated with aseptic meningitis and acute flaccid paralysis (AFP). But some infections, sometimes most of them, are asymptomatic. The mechanism of E6 virulence is unknown. Analyses of the molecular evolution of asymptomatic E6 may help understand why the infections show different manifestations. METHODS: Ninety-six stool samples of healthy children in Yunnan, China were collected and two E6 strains were isolated from them...
July 25, 2017: Virology Journal
https://www.readbyqxmd.com/read/28742792/evidence-for-genetic-association-between-chromosome-1q-loci-and-predisposition-to-colorectal-neoplasia
#15
Stephanie A Schubert, Dina Ruano, Fadwa A Elsayed, Arnoud Boot, Stijn Crobach, Arantza Farina Sarasqueta, Bruce Wolffenbuttel, Melanie M van der Klauw, Jan Oosting, Carli M Tops, Ronald van Eijk, Hans Fa Vasen, Rolf Ham Vossen, Maartje Nielsen, Sergi Castellví-Bel, Clara Ruiz-Ponte, Ian Tomlinson, Malcolm G Dunlop, Pavel Vodicka, Juul T Wijnen, Frederik J Hes, Hans Morreau, Noel Fcc de Miranda, Rolf H Sijmons, Tom van Wezel
BACKGROUND: A substantial fraction of familial colorectal cancer (CRC) and polyposis heritability remains unexplained. This study aimed to identify predisposing loci in patients with these disorders. METHODS: Homozygosity mapping was performed using 222 563 SNPs in 302 index patients with various colorectal neoplasms and 3367 controls. Linkage analysis, exome and whole-genome sequencing were performed in a family affected by microsatellite stable CRCs. Candidate variants were genotyped in 10 554 cases and 21 480 controls...
July 25, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28742110/evaluation-of-exome-variants-using-the-ion-proton-platform-to-sequence-error-prone-regions
#16
Heewon Seo, Yoomi Park, Byung Joo Min, Myung Eui Seo, Ju Han Kim
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58...
2017: PloS One
https://www.readbyqxmd.com/read/28742023/genome-wide-identification-of-lineage-and-locus-specific-variation-associated-with-pneumococcal-carriage-duration
#17
John A Lees, Nicholas J Croucher, David Goldblatt, François Nosten, Julian Parkhill, Claudia Turner, Paul Turner, Stephen D Bentley
Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%...
July 25, 2017: ELife
https://www.readbyqxmd.com/read/28742021/resolving-the-prevalence-of-somatic-transposition-in-drosophila
#18
Christoph Daniel Treiber, Scott Waddell
Somatic transposition in mammals and insects could increase cellular diversity and neural mobilization has been implicated in age-dependent decline. To understand the impact of transposition in somatic cells it is essential to reliably measure the frequency and map locations of new insertions. Here we identified thousands of putative somatic transposon insertions in neurons from individual Drosophila melanogaster using whole-genome sequencing. However, the number of de novo insertions did not correlate with transposon expression or fly age...
July 25, 2017: ELife
https://www.readbyqxmd.com/read/28741995/merdimonas-faecis-gen-nov-sp-nov-isolated-from-human-faeces
#19
Boram Seo, Ju Eun Yoo, Yung Mi Lee, GwangPyo Ko
A strictly anaerobic Gram-stain-positive, non-motile and non-spore-forming bacterial strain, BR31T, was isolated from a faecal sample of a healthy human. Bacterial colonies were ivory-coloured on GAM agar and composed of rod-shaped cells with rounded ends approximately 1.4-2.1×0.5-0.6 µm in size. According to comparative analysis based on 16S rRNA gene sequences, strain BR31T formed a distinct phylogenetic lineage that reflects a new genus within Clostridium cluster XIVa in the family Lachnospiraceae, with highest similarity to Eubacterium contortum DSM 3982T (94...
July 26, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28741255/genetics-of-schizophrenia-ready-to-translate
#20
REVIEW
Claire Foley, Aiden Corvin, Shigeki Nakagome
PURPOSE OF REVIEW: This is an era where we have significantly advanced the understanding of the genetic architecture of schizophrenia. In this review, we consider how this knowledge may translate into advances that will improve patient care. RECENT FINDINGS: Large-scale genome-wide association studies (GWAS) have identified more than a hundred loci each making a small contribution to illness risk. Meta-analysis of copy number variants (CNVs) in the Psychiatric Genomics Consortium (PGC) dataset has confirmed that some variants have a moderate or large impact on risk, although these are rare in the population...
September 2017: Current Psychiatry Reports
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