keyword
MENU ▼
Read by QxMD icon Read
search

Whole genome sequencing

keyword
https://www.readbyqxmd.com/read/28938721/the-draft-genome-sequence-of-a-desert-tree-populus-pruinosa
#1
Wenlu Yang, Kun Wang, Jian Zhang, Jianchao Ma, Jianquan Liu, Tao Ma
Populus pruinosa is a large tree that grows in deserts and shows distinct differences in both morphology and adaptation compared to its sister species, P. euphratica. Here we present a draft genome sequence for P. pruinosa and examine genomic variations between the 2 species. A total of 60 Gb of clean reads from whole-genome sequencing of a P. pruinosa individual were generated using the Illumina HiSeq2000 platform. The assembled genome is 479.3 Mb in length, with an N50 contig size of 14.0 kb and a scaffold size of 698...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#2
Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mengcheng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#3
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938470/genetic-disruption-of-21-hydroxylase-in-zebrafish-causes-interrenal-hyperplasia
#4
Helen Eachus, Andreas Zaucker, James A Oakes, Aliesha Griffin, Meltem Weger, Tülay Güran, Angela Taylor, Abigail Harris, Andy Greenfield, Jonathan L Quanson, Karl-Heinz Storbeck, Vincent T Cunliffe, Ferenc Müller, Nils Krone
Congenital adrenal hyperplasia is a group of common inherited disorders leading to glucocorticoid deficiency. Most cases are caused by 21-hydroxylase deficiency (21OHD). The systemic consequences of imbalanced steroid hormone biosynthesis due to severe 21OHD remains poorly understood. Therefore, we have developed a zebrafish model for 21OHD, which focuses on the impairment of glucocorticoid biosynthesis. A single 21-hydroxylase gene (cyp21a2) is annotated in the zebrafish genome based on sequence homology. Our in silico analysis of the Cyp21a2 protein sequence suggests a sufficient degree of similarity for the usage of zebrafish cyp21a2 to model aspects of human 21OHD in vivo...
September 13, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938154/massively-parallel-sequencing-of-forensic-strs-and-snps-using-the-illumina-%C3%A2-forenseq%C3%A2-dna-signature-prep-kit-on-the-miseq-fgx%C3%A2-forensic-genomics-system
#5
Fei Guo, Jiao Yu, Lu Zhang, Jun Li
The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples)...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28937735/whole-genome-shotgun-sequencing-and-comparison-of-two-%C3%AE-proteobacterial-species-in-search-of-the-bulgecin-biosynthetic-cluster
#6
Mark E Horsman, Daniel R Marous, Rongfeng Li, Ryan A Oliver, Byungjin Byun, Scott J Emrich, Bill Boggess, Craig A Townsend, Shahriar Mobashery
We have produced draft whole-genome sequences for two bacterial strains reported to produce the bulgecins as well as NRPS-derived monobactam β-lactam antibiotics. We propose reclassification of ATCC 31363 from the original Pseudomonas genus to Paraburkholderia acidophila. We further reaffirm that ATCC 31433 (Burkholderia mesoacidophila) is a taxonomically distinct producer of bulgecins with notable gene regions shared with Paraburkholderia acidophila. We use RAST multiple gene comparison and MASH distancing with published genomes to order the draft contigs and identify unique gene regions for characterization...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28936424/acid-stress-response-mechanisms-of-group-b-streptococci
#7
REVIEW
Sarah Shabayek, Barbara Spellerberg
Group B streptococcus (GBS) is a leading cause of neonatal mortality and morbidity in the United States and Europe. It is part of the vaginal microbiota in up to 30% of pregnant women and can be passed on to the newborn through perinatal transmission. GBS has the ability to survive in multiple different host niches. The pathophysiology of this bacterium reveals an outstanding ability to withstand varying pH fluctuations of the surrounding environments inside the human host. GBS host pathogen interations include colonization of the acidic vaginal mucosa, invasion of the neutral human blood or amniotic fluid, breaching of the blood brain barrier as well as survival within the acidic phagolysosomal compartment of macrophages...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28936210/novel-mutations-of-the-tetratricopeptide-repeat-domain-7a-gene-and-phenotype-genotype-comparison
#8
Reyin Lien, Yung-Feng Lin, Min-Wei Lai, Hui-Ying Weng, Ren-Chin Wu, Tang-Her Jaing, Jing-Long Huang, Shih-Feng Tsai, Wen-I Lee
The gastrointestinal tract contains the largest lymphoid organ to react with pathogenic microorganisms and suppress excess inflammation. Patients with primary immunodeficiency diseases (PIDs) can suffer from refractory diarrhea. In this study, we present two siblings who began to suffer from refractory diarrhea with a poor response to aggressive antibiotic and immunosuppressive treatment after surgical release of neonatal intestinal obstruction. Their lymphocyte proliferation was low, but superoxide production and IL-10 signaling were normal...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28936078/clinical-and-genetic-characteristics-of-leukodystrophies-in-africa
#9
REVIEW
Mutaz Amin, Liena Elsayed, Ammar Eltahir Ahmed
Recent understanding of the genetic basis of neurological disorders in Africa has grown rapidly in the last two decades. Africa harbors the largest genetic repertoire in the world which gives unique opportunity to discover novel variant, genes, and molecular pathways associated with various neurological diseases. Despite that, large-scale genomic and exome studies are severely lacking especially for neglected diseases such as leukodystrophies. This review aims to shed light on the currently developed research in leukodystrophies in Africa...
August 2017: Journal of Neurosciences in Rural Practice
https://www.readbyqxmd.com/read/28935873/whole-genome-sequencing-molecular-typing-and-in-vivo-virulence-of-oxa-48-producing-escherichia-coli-isolates-including-st131-h30-rx-h22-and-h41-subclones
#10
María de Toro, Javier Fernández, Vanesa García, Azucena Mora, Jorge Blanco, Fernando de la Cruz, M Rosario Rodicio
Carbapenem-resistant Enterobacteriaceae, including the increasingly reported OXA-48 Escherichia coli producers, are an emerging public health threat worldwide. Due to their alarming detection in our healthcare setting and their possible presence in the community, seven OXA-48-producing, extraintestinal pathogenic E. coli were analysed by whole genome sequencing as well as conventional tools, and tested for in vivo virulence. As a result, five E. coli OXA-48-producing subclones were detected (O25:H4-ST131/PST43-fimH30-virotype E; O25:H4-ST131/PST9-fimH22-virotype D5, O16:H5-ST131/PST506-fimH41; O25:H5-ST83/PST207 and O9:H25-ST58/PST24)...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935752/erratum-for-halpin-et-al-finished-whole-genome-sequences-of-clostridium-butyricum-toxin-subtype-e4-and-clostridium-baratii-toxin-subtype-f7-strains
#11
Jessica L Halpin, Karen Hill, Shannon L Johnson, David Carlton Bruce, T Brian Shirey, Janet K Dykes, Carolina Lúquez
No abstract text is available yet for this article.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935746/complete-genome-sequence-of-a-novel-bioflocculant-producing-strain-microbacterium-paludicola-cc3
#12
Weijie Liu, Cong Liu, Di Sun
Microbacterium paludicola CC3 exhibits the capability to produce polysaccharide bioflocculants. Here, we report the whole-genome sequence of M. paludicola CC3, which may be helpful in understanding the genetic basis of the biosynthesis of polysaccharide bioflocculants as well as in promoting its production and application in industrial fields.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935731/draft-genome-sequence-of-aspergillus-persii-nibrfgc000004109-which-has-antibacterial-activity-against-plant-pathogenic-bacteria
#13
Jung A Kim, Jongbum Jeon, Sook-Young Park, Ki-Tae Kim, Gobong Choi, Hoa Thi Nguyen, Sun Jeong Jeon, Hyang Burm Lee, Chang-Hwan Bae, Hee-Sun Yang, Joo-Hong Yeo, Jin-Cheol Kim, Yong-Hwan Lee, Soonok Kim
The fungus Aspergillus persii strain NIBRFGC000004109 is capable of producing penicillic acid and showed antibacterial activity against various plant-pathogenic bacteria, including Xanthomonas arboricola pv. pruni. Here, we report the first draft whole-genome sequence of A. persii The assembly comprises 38,414,373 bp, with 12 scaffolds.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935481/stalking-a-lethal-superbug-by-whole-genome-sequencing-and-phylogenetics-influence-on-unraveling-a-major-hospital-outbreak-of-carbapenem-resistant-klebsiella-pneumoniae
#14
Thorsten Kaiser, Knut Finstermeier, Madlen Häntzsch, Sarah Faucheux, Martin Kaase, Tim Eckmanns, Sven Bercker, Udo X Kaisers, Norman Lippmann, Arne C Rodloff, Joachim Thiery, Christoph Lübbert
BACKGROUND: From July 2010-April 2013, Leipzig University Hospital experienced the largest outbreak of a Klebsiella pneumoniae carbapenemase 2 (KPC-2)-producing Klebsiella pneumoniae (KPC-2-Kp) strain observed in Germany to date. After termination of the outbreak, we aimed to reconstruct transmission pathways by phylogenetics based on whole-genome sequencing (WGS). METHODS: One hundred seventeen KPC-2-Kp isolates from 89 outbreak patients, 5 environmental KPC-2-Kp isolates, and 24 K pneumoniae strains not linked to the outbreak underwent WGS...
September 18, 2017: American Journal of Infection Control
https://www.readbyqxmd.com/read/28934986/identification-of-novel-candidate-disease-genes-from-de-novo-exonic-copy-number-variants
#15
Tomasz Gambin, Bo Yuan, Weimin Bi, Pengfei Liu, Jill A Rosenfeld, Zeynep Coban-Akdemir, Amber N Pursley, Sandesh C S Nagamani, Ronit Marom, Sailaja Golla, Lauren Dengle, Heather G Petrie, Reuben Matalon, Lisa Emrick, Monica B Proud, Diane Treadwell-Deering, Hsiao-Tuan Chao, Hannele Koillinen, Chester Brown, Nora Urraca, Roya Mostafavi, Saunder Bernes, Elizabeth R Roeder, Kimberly M Nugent, Patricia I Bader, Gary Bellus, Michael Cummings, Hope Northrup, Myla Ashfaq, Rachel Westman, Robert Wildin, Anita E Beck, LaDonna Immken, Lindsay Elton, Shaun Varghese, Edward Buchanan, Laurence Faivre, Mathilde Lefebvre, Christian P Schaaf, Magdalena Walkiewicz, Yaping Yang, Sung-Hae L Kang, Seema R Lalani, Carlos A Bacino, Arthur L Beaudet, Amy M Breman, Janice L Smith, Sau Wai Cheung, James R Lupski, Ankita Patel, Chad A Shaw, Paweł Stankiewicz
BACKGROUND: Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017...
September 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28934964/comprehensive-benchmarking-and-ensemble-approaches-for-metagenomic-classifiers
#16
Alexa B R McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J Prill, Elizabeth Hénaff, Noah Alexander, Samuel S Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi, Nick Greenfield, Rita R Colwell, Gail L Rosen, Christopher E Mason
BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934948/multi-breed-genomic-prediction-using-bayes-r-with-sequence-data-and-dropping-variants-with-a-small-effect
#17
Irene van den Berg, Phil J Bowman, Iona M MacLeod, Ben J Hayes, Tingting Wang, Sunduimijid Bolormaa, Mike E Goddard
BACKGROUND: The increasing availability of whole-genome sequence data is expected to increase the accuracy of genomic prediction. However, results from simulation studies and analysis of real data do not always show an increase in accuracy from sequence data compared to high-density (HD) single nucleotide polymorphism (SNP) chip genotypes. In addition, the sheer number of variants makes analysis of all variants and accurate estimation of all effects computationally challenging. Our objective was to find a strategy to approximate the analysis of whole-sequence data with a Bayesian variable selection model...
September 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28934930/xcavator-accurate-detection-and-genotyping-of-copy-number-variants-from-second-and-third-generation-whole-genome-sequencing-experiments
#18
Alberto Magi, Tommaso Pippucci, Carlo Sidore
BACKGROUND: We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS: By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it to the analysis Illumina and Pacific Bioscencies data and we compared its performance to other ten state of the art tools...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934671/the-hnf1a-mutant-ala180val-clinical-challenges-in-determining-causality-of-a-rare-hnf1a-variant-in-familial-diabetes
#19
J V Sagen, L Bjørkhaug, B I Haukanes, L Grevle, J Molnes, B G Nedrebø, O Søvik, P R Njølstad, S Johansson, A Molven
AIMS: Heterozygous mutations in hepatocyte nuclear factor-1A (HNF1A) cause maturity-onset diabetes of the young type 3 (MODY3). Our aim was to compare two families with suspected dominantly inherited diabetes and a new HNF1A variant of unknown clinical significance. METHODS: The HNF1A gene was sequenced in two independently recruited families from the Norwegian MODY Registry. Both familes were phenotyped clinically and biochemically. Microsatellite markers around and within the HNF1A locus were used for haplotyping...
September 1, 2017: Diabetes Research and Clinical Practice
https://www.readbyqxmd.com/read/28934422/low-frequency-of-acquired-isoniazid-and-rifampicin-resistance-in-rifampicin-susceptible-pulmonary-tuberculosis-in-a-setting-of-high-hiv-1-infection-and-tuberculosis-coprevalence
#20
Neesha Rockwood, Frederick Sirgel, Elizabeth Streicher, Robin Warren, Graeme Meintjes, Robert J Wilkinson
Background: We estimated the incidence of acquired isoniazid and rifampicin resistance in rifampicin-susceptible tuberculosis in a setting of high human immunodeficiency virus type 1 (HIV-1) infection and tuberculosis coprevalence. Methods: GeneXpert MTB/RIF-confirmed patients with rifampicin-susceptible tuberculosis were recruited at antituberculosis treatment initiation in Khayelitsha, South Africa. Liquid culture and adherence assessment were performed at 2 and 5-6 months...
September 15, 2017: Journal of Infectious Diseases
keyword
keyword
24601
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"