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Whole-genome sequencing

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https://www.readbyqxmd.com/read/29792754/loss-of-chromosome-18q11-2-q12-1-is-predictive-for-survival-in-patients-with-metastatic-colorectal-cancer-treated-with-bevacizumab
#1
Erik van Dijk, Hedde D Biesma, Martijn Cordes, Dominiek Smeets, Maarten Neerincx, Sudipto Das, Paul P Eijk, Verena Murphy, Anna Barat, Orna Bacon, Jochen H M Prehn, Johannes Betge, Timo Gaiser, Bozena Fender, Gerrit A Meijer, Deborah A McNamara, Rut Klinger, Miriam Koopman, Matthias P A Ebert, Elaine W Kay, Bryan T Hennessey, Henk M W Verheul, William M Gallagher, Darran P O'Connor, Cornelis J A Punt, Fotios Loupakis, Diether Lambrechts, Annette T Byrne, Nicole C T van Grieken, Bauke Ylstra
Purpose Patients with metastatic colorectal cancer (mCRC) have limited benefit from the addition of bevacizumab to standard chemotherapy. However, a subset probably benefits substantially, highlighting an unmet clinical need for a biomarker of response to bevacizumab. Previously, we demonstrated that losses of chromosomes 5q34, 17q12, and 18q11.2-q12.1 had a significant correlation with progression-free survival (PFS) in patients with mCRC treated with bevacizumab in the CAIRO2 clinical trial but not in patients who did not receive bevacizumab in the CAIRO trial...
May 24, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29792591/comprehensive-evolutionary-and-phylogenetic-analysis-of-hepacivirus-n-hnv
#2
M S da Silva, D M Junqueira, L F Baumbach, S P Cibulski, A C S Mósena, M N Weber, S Silveira, G M de Moraes, R D Maia, V C S Coimbra, C W Canal
Hepaciviruses (HVs) have been detected in several domestic and wild animals and present high genetic diversity. The actual classification divides the genus Hepacivirus into 14 species (A-N), according to their phylogenetic relationships, including the bovine hepacivirus [Hepacivirus N (HNV)]. In this study, we confirmed HNV circulation in Brazil and sequenced the whole genome of two strains. Based on the current classification of HCV, which is divided into genotypes and subtypes, we analysed all available bovine hepacivirus sequences in the GenBank database and proposed an HNV classification...
May 24, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29792182/boostme-accurately-predicts-dna-methylation-values-in-whole-genome-bisulfite-sequencing-of-multiple-human-tissues
#3
Luli S Zou, Michael R Erdos, D Leland Taylor, Peter S Chines, Arushi Varshney, Stephen C J Parker, Francis S Collins, John P Didion
BACKGROUND: Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage sites may mitigate these biases while also identifying important genomic features associated with predictive power. RESULTS: Here we describe BoostMe, a method for imputing low-quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#4
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29791438/identity-by-descent-analyses-for-measuring-population-dynamics-and-selection-in-recombining-pathogens
#5
Lyndal Henden, Stuart Lee, Ivo Mueller, Alyssa Barry, Melanie Bahlo
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections...
May 23, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29790980/contrasting-patterns-of-genomic-diversity-reveal-accelerated-genetic-drift-but-reduced-directional-selection-on-x-chromosome-in-wild-and-domestic-sheep-species
#6
Ze-Hui Chen, Min Zhang, Feng-Hua Lv, Xue Ren, Wen-Rong Li, Ming-Jun Liu, Kiwoong Nam, Michael W Bruford, Meng-Hua Li
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29790871/phenotypic-expansion-illuminates-multilocus-pathogenic-variation
#7
Ender Karaca, Jennifer E Posey, Zeynep Coban Akdemir, Davut Pehlivan, Tamar Harel, Shalini N Jhangiani, Yavuz Bayram, Xiaofei Song, Vahid Bahrambeigi, Ozge Ozalp Yuregir, Sevcan Bozdogan, Gozde Yesil, Sedat Isikay, Donna Muzny, Richard A Gibbs, James R Lupski
PurposeMultilocus variation-pathogenic variants in two or more disease genes-can potentially explain the underlying genetic basis for apparent phenotypic expansion in cases for which the observed clinical features extend beyond those reported in association with a "known" disease gene.MethodsAnalyses focused on 106 patients, 19 for whom apparent phenotypic expansion was previously attributed to variation at known disease genes. We performed a retrospective computational reanalysis of whole-exome sequencing data using stringent Variant Call File filtering criteria to determine whether molecular diagnoses involving additional disease loci might explain the observed expanded phenotypes...
April 26, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29790460/establishment-of-the-european-meningococcal-strain-collection-genome-library-emsc-gl-for-the-2011-to-2012-epidemiological-year
#8
Holly B Bratcher, Carina Brehony, Sigrid Heuberger, Despo Pieridou-Bagatzouni, Pavla Křížová, Steen Hoffmann, Maija Toropainen, Muhamed-Kheir Taha, Heike Claus, Georgina Tzanakaki, Tímea Erdôsi, Jelena Galajeva, Arie van der Ende, Anna Skoczyńska, Marina Pana, Alena Vaculíková, Metka Paragi, Martin Cj Maiden, Dominique A Caugant
Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011-June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance...
May 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29790070/genotyping-single-sperm-cells-by-universal-marsala-enables-the-acquisition-of-linkage-information-for-combined-pre-implantation-genetic-diagnosis-and-genome-screening
#9
Haitao Wu, Xiaoting Shen, Lei Huang, Yanhong Zeng, Yumei Gao, Lin Shao, Baomin Lu, Yiping Zhong, Benyu Miao, Yanwen Xu, Yali Wang, Yubin Li, Luoxing Xiong, Sijia Lu, X Sunney Xie, Canquan Zhou
PURPOSE: This paper aims to investigate the feasibility of performing pre-implantation genetic diagnosis (PGD) and pre-implantation genetic screening (PGS) simultaneously by a universal strategy without the requirement of genotyping relevant affected family members or lengthy preliminary work on linkage analysis. METHODS: By utilizing a universal Mutated Allele Revealed by Sequencing with Aneuploidy and Linkage Analyses (MARSALA) strategy based on low depth whole genome sequencing (~3x), not involving specific primers' design nor the enrichment of SNP markers for haplotype construction...
May 22, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29789942/analysis-of-the-complete-genome-sequence-of-a-potyvirus-from-passion-fruit-suggests-its-taxonomic-classification-as-a-member-of-a-new-species
#10
Ke Yang, Haixia Yan, Li Song, Pengfei Jin, Weiguo Miao, Hongguang Cui
The complete genomic sequence of a telosma mosaic virus (TeMV) isolate (named PasFru), identified in passion fruit in China, was determined. The entire RNA genome of PasFru comprises 10,049 nucleotides (nt) excluding the poly(A) tail and encodes a polyprotein of 3,173 amino acids (aa), flanked by 5' and 3' untranslated regions (UTR) of 276 and 251 nt, respectively. Compared with the previous TeMV isolate Hanoi from Telosma cordata, the only documented isolate with the entire genome sequence annotated, PasFru had an extra 87 nt and 89 aa residues at the 3'-end of 5'UTR and the N-terminus of the P1 protein, respectively, which contributed to the genome size difference between PasFru and Hanoi (10,049 nt versus 9,689 nt)...
May 22, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29789557/measuring-coverage-and-accuracy-of-whole-exome-sequencing-in-clinical-context
#11
Sek Won Kong, In-Hee Lee, Xuanshi Liu, Joel N Hirschhorn, Kenneth D Mandl
PurposeTo evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors.MethodsBlood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio.ResultsMean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability...
April 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29789467/the-present-and-future-of-whole-genome-sequencing-wgs-and-whole-metagenome-sequencing-wms-for-surveillance-of-antimicrobial-resistant-microorganisms-and-antimicrobial-resistance-genes-across-the-food-chain
#12
REVIEW
Elena A Oniciuc, Eleni Likotrafiti, Adrián Alvarez-Molina, Miguel Prieto, Jesús A Santos, Avelino Alvarez-Ordóñez
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain...
May 22, 2018: Genes
https://www.readbyqxmd.com/read/29789419/detection-of-bladder-cancer-via-microfluidic-immunoassay-and-single-cell-dna-copy-number-alteration-analysis-of-captured-urinary-exfoliated-tumor-cells
#13
Anqi Chen, Guanghou Fu, Zhijie Xu, Yukun Sun, Xiaoyi Chen, Kok Suen Cheng, Kuang Hong Neoh, Zhewen Tang, Shifu Chen, Ming Liu, Tanxiao Huang, Yun Dai, Qibo Wang, Jing Jin, Baiye Jin, Ray P S Han
The increasing incidence of bladder cancer (BC) and its high rate of recurrence over a 5-year period necessitate the need for diagnosis and surveillance amelioration. Cystoscopy and urinary cytology are the current tools, and molecular techniques such as BTA stat, NMP22, survivin mRNA, and urovysion FISH have attracted attention, however, they suf-fer from insufficient sensitivity or specificity. We developed a novel microfluidic approach for harvesting intact urinary-exfoliated tumor cells (UETCs), either individually or in clus-ters, in a clean and segregated environment, which is crucial to minimize cross-contamination and misreads...
May 22, 2018: Cancer Research
https://www.readbyqxmd.com/read/29789361/breaching-pathogeographic-barriers-by-the-bat-white-nose-fungus
#14
Johanna Rhodes, Matthew C Fisher
Bat white-nose syndrome has become associated with unparalleled mortality in bat species across the United States since 2006. In a recent article, Drees and colleagues (mBio 8:e01941-17, 2017, https://doi.org/10.1128/mBio.01941-17) utilized both whole-genome sequencing and microsatellite data to explore the origin and spread of the causative agent of bat white-nose syndrome, Pseudogymnoascus destructans The research by Drees et al. supports the hypothesis that P. destructans was introduced into North America from Europe, with molecular dating suggesting a divergence from European isolates approximately 100 years ago...
May 22, 2018: MBio
https://www.readbyqxmd.com/read/29789313/blast-xyplot-viewer-a-tool-for-performing-blast-in-whole-genome-sequenced-bacteria-archaea-and-visualize-whole-results-simultaneously
#15
Yagul Pedraza-Pérez, Rodrigo Alberto Cuevas-Vede, Ángel Bernardo Canto-Gómez, Liliana López-Pliego, Rosa María Gutiérrez-Ríos, Ismael Hernández-Lucas, Gustavo Rubín-Linares, Ygnacio Martínez-Laguna, Jesús Francisco López-Olguín, Luis Ernesto Fuentes-Ramírez
One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x -axis and the number of replicon used on the y -axis...
May 22, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29789182/geodermatophilus-chilensis-sp-nov-from-soil-of-the-yungay-core-region-of-the-atacama-desert-chile
#16
Jean Franco Castro, Imen Nouioui, Vartul Sangal, Martha E Trujillo, Maria Del Carmen Montero-Calasanz, Tara Rahmani, Alan T Bull, Juan A Asenjo, Barbara A Andrews, Michael Goodfellow
A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T , B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus...
April 4, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29788909/whole-genome-analysis-reveals-the-diversity-and-evolutionary-relationships-between-necrotic-enteritis-causing-strains-of-clostridium-perfringens
#17
Jake A Lacey, Theodore R Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I Rood, Ben Wade, Anthony L Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A Johanesen, Dena Lyras, Robert J Moore
BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788905/genomic-prediction-of-the-polled-and-horned-phenotypes-in-merino-sheep
#18
Naomi Duijvesteijn, Sunduimijid Bolormaa, Hans D Daetwyler, Julius H J van der Werf
BACKGROUND: In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene...
May 22, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29788454/variation-in-human-chromosome-21-ribosomal-rna-genes-characterized-by-tar-cloning-and-long-read-sequencing
#19
Jung-Hyun Kim, Alexander T Dilthey, Ramaiah Nagaraja, Hee-Sheung Lee, Sergey Koren, Dawood Dudekula, William H Wood Iii, Yulan Piao, Aleksey Y Ogurtsov, Koichi Utani, Vladimir N Noskov, Svetlana A Shabalina, David Schlessinger, Adam M Phillippy, Vladimir Larionov
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788374/presence-of-hpv-apobec-related-minority-variants-in-hpv16-genomes-from-anal-and-cervical-samples-but-not-in-hpv52-and-hpv58
#20
Alice-Andrée Mariaggi, Hélène Péré, Marine Perrier, Benoit Visseaux, Gilles Collin, David Veyer, Quentin Le Hingrat, Valentine Marie Ferré, Véronique Joly, Anne Couvelard, Margot Bucau, Carine Davitian, Diane Descamps, Laurent Abramowitz, Charlotte Charpentier
Background: The aim of this study was to investigate the presence of minority variants (MV) in high-risk Human Papillomavirus types (hrHPV16, HPV52, HPV58) from cervical and anal smears. Methods: Whole HPV genome ultra-deep sequencing (UDS) was performed on cervical and anal smears collected during patients' follow-up. Bioinformatics analyses were performed using Bowtie2® (Geneious®). Results: We assessed 55 HPV16+, 20 HPV52+ and 17 HPV58+ samples, with significant differences in patient characteristics for the two anatomic sites...
May 17, 2018: Journal of Infectious Diseases
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