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https://www.readbyqxmd.com/read/27897270/trueprime-is-a-novel-method-for-whole-genome-amplification-from-single-cells-based-on-tthprimpol
#1
Ángel J Picher, Bettina Budeus, Oliver Wafzig, Carola Krüger, Sara García-Gómez, María I Martínez-Jiménez, Alberto Díaz-Talavera, Daniela Weber, Luis Blanco, Armin Schneider
Sequencing of a single-cell genome requires DNA amplification, a process prone to introducing bias and errors into the amplified genome. Here we introduce a novel multiple displacement amplification (MDA) method based on the unique DNA primase features of Thermus thermophilus (Tth) PrimPol. TthPrimPol displays a potent primase activity preferring dNTPs as substrates unlike conventional primases. A combination of TthPrimPol's unique ability to synthesize DNA primers with the highly processive Phi29 DNA polymerase (Φ29DNApol) enables near-complete whole genome amplification from single cells...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27881071/genome-wide-analyses-of-chitin-synthases-identify-horizontal-gene-transfers-towards-bacteria-and-allow-a-robust-and-unifying-classification-into-fungi
#2
Isabelle R Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara, Mathias Choquer
BACKGROUND: Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate...
November 24, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27874022/in-depth-comparison-of-somatic-point-mutation-callers-based-on-different-tumor-next-generation-sequencing-depth-data
#3
Lei Cai, Wei Yuan, Zhou Zhang, Lin He, Kuo-Chen Chou
Four popular somatic single nucleotide variant (SNV) calling methods (Varscan, SomaticSniper, Strelka and MuTect2) were carefully evaluated on the real whole exome sequencing (WES, depth of ~50X) and ultra-deep targeted sequencing (UDT-Seq, depth of ~370X) data. The four tools returned poor consensus on candidates (only 20% of calls were with multiple hits by the callers). For both WES and UDT-Seq, MuTect2 and Strelka obtained the largest proportion of COSMIC entries as well as the lowest rate of dbSNP presence and high-alternative-alleles-in-control calls, demonstrating their superior sensitivity and accuracy...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27863959/transmission-of-staphylococcus-aureus-between-health-care-workers-the-environment-and-patients-in-an-intensive-care-unit-a-longitudinal-cohort-study-based-on-whole-genome-sequencing
#4
James R Price, Kevin Cole, Andrew Bexley, Vasiliki Kostiou, David W Eyre, Tanya Golubchik, Daniel J Wilson, Derrick W Crook, A Sarah Walker, Timothy E A Peto, Martin J Llewelyn, John Paul
BACKGROUND: Health-care workers have been implicated in nosocomial outbreaks of Staphylococcus aureus, but the dearth of evidence from non-outbreak situations means that routine health-care worker screening and S aureus eradication are controversial. We aimed to determine how often S aureus is transmitted from health-care workers or the environment to patients in an intensive care unit (ICU) and a high-dependency unit (HDU) where standard infection control measures were in place. METHODS: In this longitudinal cohort study, we systematically sampled health-care workers, the environment, and patients over 14 months at the ICU and HDU of the Royal Sussex County Hospital, Brighton, England...
November 15, 2016: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/27826616/development-and-validation-of-an-ultra-high-sensitive-next-generation-sequencing-assay-for-molecular-diagnosis-of-clinical-oncology
#5
Jiao Liang, Yaoguang She, Jiaqi Zhu, Longgang Wei, Lanying Zhang, Lianju Gao, Yan Wang, Jing Xing, Yang Guo, Xuehong Meng, Peiyu Li
Dramatic improvements in the understanding of oncogenes have spurred the development of molecular target therapies, which created an exigent need for comprehensive and rapid clinical genotyping. Next-generation sequencing (NGS) assay with increased performance and decreased cost is becoming more widely used in clinical diagnosis. However, the optimization and validation of NGS assay remain a challenge, especially for the detection of somatic variants at low mutant allele fraction (MAF). In the present study, we developed and validated the Novogene Comprehensive Panel (NCP) based on targeted capture for NGS analysis...
November 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27822544/multiplexed-metagenomic-deep-sequencing-to-analyze-the-composition-of-high-priority-pathogen-reagents
#6
Michael R Wilson, Greg Fedewa, Mark D Stenglein, Judith Olejnik, Linda J Rennick, Sham Nambulli, Friederike Feldmann, W Paul Duprex, John H Connor, Elke Mühlberger, Joseph L DeRisi
Laboratories studying high-priority pathogens need comprehensive methods to confirm microbial species and strains while also detecting contamination. Metagenomic deep sequencing (MDS) inventories nucleic acids present in laboratory stocks, providing an unbiased assessment of pathogen identity, the extent of genomic variation, and the presence of contaminants. Double-stranded cDNA MDS libraries were constructed from RNA extracted from in vitro-passaged stocks of six viruses (La Crosse virus, Ebola virus, canine distemper virus, measles virus, human respiratory syncytial virus, and vesicular stomatitis virus)...
July 2016: MSystems
https://www.readbyqxmd.com/read/27814745/deep-targeted-sequencing-of-12-breast-cancer-susceptibility-regions-in-4611-women-across-four-different-ethnicities
#7
Sara Lindström, Akweley Ablorh, Brad Chapman, Alexander Gusev, Gary Chen, Constance Turman, A Heather Eliassen, Alkes L Price, Brian E Henderson, Loic Le Marchand, Oliver Hofmann, Christopher A Haiman, Peter Kraft
BACKGROUND: Although genome-wide association studies (GWASs) have identified thousands of disease susceptibility regions, the underlying causal mechanism in these regions is not fully known. It is likely that the GWAS signal originates from one or many as yet unidentified causal variants. METHODS: Using next-generation sequencing, we characterized 12 breast cancer susceptibility regions identified by GWASs in 2288 breast cancer cases and 2323 controls across four populations of African American, European, Japanese, and Hispanic ancestry...
November 5, 2016: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/27807179/genome-scale-characterization-of-rna-tertiary-structures-and-their-functional-impact-by-rna-solvent-accessibility-prediction
#8
Yuedong Yang, Xiaomei Li, Huiying Zhao, Jian Zhan, Jihua Wang, Yaoqi Zhou
As most RNA structures are elusive to structure determination, obtaining solvent accessible surface areas (ASA) of nucleotides in an RNA structure is an important first step to characterize potential functional sites and core structural regions. Here, we developed RNAsnap, the first machine-learning method trained on protein-bound RNA structures for solvent accessibility prediction. Built on sequence profiles from multiple sequence alignment (RNAsnap-prof), the method provided robust prediction in five-fold cross-validation and an independent test (Pearson correlation coefficients, r, between predicted and actual ASA values are 0...
November 2, 2016: RNA
https://www.readbyqxmd.com/read/27799064/mipep-recessive-variants-cause-a-syndrome-of-left-ventricular-non-compaction-hypotonia-and-infantile-death
#9
Mohammad K Eldomery, Zeynep C Akdemir, F-Nora Vögtle, Wu-Lin Charng, Patrycja Mulica, Jill A Rosenfeld, Tomasz Gambin, Shen Gu, Lindsay C Burrage, Aisha Al Shamsi, Samantha Penney, Shalini N Jhangiani, Holly H Zimmerman, Donna M Muzny, Xia Wang, Jia Tang, Ravi Medikonda, Prasanna V Ramachandran, Lee-Jun Wong, Eric Boerwinkle, Richard A Gibbs, Christine M Eng, Seema R Lalani, Jozef Hertecant, Richard J Rodenburg, Omar A Abdul-Rahman, Yaping Yang, Fan Xia, Meng C Wang, James R Lupski, Chris Meisinger, V Reid Sutton
BACKGROUND: Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease. METHODS: Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC), developmental delay (DD), seizures, and severe hypotonia...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27794038/multivariate-analysis-of-hemicelluloses-in-bleached-kraft-pulp-using-infrared-spectroscopy
#10
Zhiwen Chen, Thomas Q Hu, Ho Fan Jang, Edward Grant
The hemicellulose composition of a pulp significantly affects its chemical and physical properties and thus represents an important process control variable. However, complicated steps of sample preparation make standard methods for the carbohydrate analysis of pulp samples, such as high performance liquid chromatography (HPLC), expensive and time-consuming. In contrast, pulp analysis by attenuated total internal reflection Fourier transform infrared spectroscopy (ATR FT-IR) requires little sample preparation...
October 28, 2016: Applied Spectroscopy
https://www.readbyqxmd.com/read/27782205/discrimination-of-transgenic-soybean-seeds-by-terahertz-spectroscopy
#11
Wei Liu, Changhong Liu, Feng Chen, Jianbo Yang, Lei Zheng
Discrimination of genetically modified organisms is increasingly demanded by legislation and consumers worldwide. The feasibility of a non-destructive discrimination of glyphosate-resistant and conventional soybean seeds and their hybrid descendants was examined by terahertz time-domain spectroscopy system combined with chemometrics. Principal component analysis (PCA), least squares-support vector machines (LS-SVM) and PCA-back propagation neural network (PCA-BPNN) models with the first and second derivative and standard normal variate (SNV) transformation pre-treatments were applied to classify soybean seeds based on genotype...
October 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27782109/joint-association-analysis-of-a-binary-and-a-quantitative-trait-in-family-samples
#12
Shuai Wang, James B Meigs, Josée Dupuis
In recent years, improved genotyping and sequencing technologies have enabled the discovery of new loci associated with various diseases or traits. For instance, by testing the association with each single-nucleotide variant (SNV) separately, genome-wide association studies (GWAS) have achieved tremendous success in identifying SNVs associated with specific traits. However, little is known about the common genetic basis of multiple traits owing to lack of efficient methods. With the use of extended quasi-likelihood, a Wald test has been proposed to perform a bivariate analysis of a continuous and a binary trait in unrelated samples...
October 26, 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27778000/improving-selectivity-in-catalytic-hydrodefluorination-by-limiting-snv-reactivity
#13
Juliane Krüger, Christian Ehm, Dieter Lentz
Catalytic hydrodefluorination of perfluoroallylbenzene with Cp2TiH in THF is unselective and yields a variety of previously unknown compounds, predominantly activated in the allylic position. Several different mechanisms have been examined in detail using solvent corrected (THF) DFT(M06-2X) calculations for the archetypal perfluorinated olefin perfluoropropene and perfluoroallylbenzene: (a) single electron transfer, (b) hydrometallation/fluoride elimination, (c) σ-bond metathesis (allylic or vinylic), and (d) nucleophilic vinylic substitution (SNV, w/o Ti-F contacts in the TS)...
October 25, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27774452/rna-sequencing-of-formalin-fixed-paraffin-embedded-specimens-for-gene-expression-quantification-and-data-mining
#14
Yan Guo, Jie Wu, Shilin Zhao, Fei Ye, Yinghao Su, Travis Clark, Quanhu Sheng, Brian Lehmann, Xiao-Ou Shu, Qiuyin Cai
Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (N = 16). We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27763552/maporal-hantavirus-causes-mild-pathology-in-deer-mice-peromyscus-maniculatus
#15
Amanda McGuire, Kaitlyn Miedema, Joseph R Fauver, Amber Rico, Tawfik Aboellail, Sandra L Quackenbush, Ann Hawkinson, Tony Schountz
Rodent-borne hantaviruses can cause two human diseases with many pathological similarities: hantavirus cardiopulmonary syndrome (HCPS) in the western hemisphere and hemorrhagic fever with renal syndrome in the eastern hemisphere. Each virus is hosted by specific reservoir species without conspicuous disease. HCPS-causing hantaviruses require animal biosafety level-4 (ABSL-4) containment, which substantially limits experimental research of interactions between the viruses and their reservoir hosts. Maporal virus (MAPV) is a South American hantavirus not known to cause disease in humans, thus it can be manipulated under ABSL-3 conditions...
October 18, 2016: Viruses
https://www.readbyqxmd.com/read/27742377/whole-genome-sequencing-discriminates-hepatocellular-carcinoma-with-intrahepatic-metastasis-from-multi-centric-tumors
#16
Mayuko Furuta, Masaki Ueno, Akihiro Fujimoto, Shinya Hayami, Satoru Yasukawa, Fumiyoshi Kojima, Koji Arihiro, Yoshiiku Kawakami, Christopher P Wardell, Yuichi Shiraishi, Hiroko Tanaka, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Naoki Tokunaga, Keith A Boroevich, Tetsuo Abe, Hiroshi Aikata, Hideki Ohdan, Kunihito Gotoh, Michiaki Kubo, Tatsuhiko Tsunoda, Satoru Miyano, Kazuaki Chayama, Hiroki Yamaue, Hidewaki Nakagawa
BACKGROUND & AIMS: Patients with hepatocellular carcinoma (HCC) have a high-risk of multi-centric (MC) tumor occurrence due to a strong carcinogenic background in the liver. In addition, they have a high risk of intrahepatic metastasis (IM). Liver tumors withIM or MC are profoundly different in their development and clinical outcome. However, clinically or pathologically discriminating between IM and MC can be challenging. This study investigated whether IM or MC could be diagnosed at the molecular level...
October 11, 2016: Journal of Hepatology
https://www.readbyqxmd.com/read/27687569/representing-and-decomposing-genomic-structural-variants-as-balanced-integer-flows-on-sequence-graphs
#17
Daniel R Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey, David Haussler
BACKGROUND: The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models. However, it has been observed that genomes are highly plastic, and that whole regions can be moved, removed or duplicated in bulk. These structural variants (SV) have been shown to have significant impact on phenotype, but their study has been held back by the combinatorial complexity of the underlying models...
September 29, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27639823/genetic-factors-of-the-disease-course-after-sepsis-rare-deleterious-variants-are-predictive
#18
Stefan Taudien, Ludwig Lausser, Evangelos J Giamarellos-Bourboulis, Christoph Sponholz, Franziska Schöneweck, Marius Felder, Lyn-Rouven Schirra, Florian Schmid, Charalambos Gogos, Susann Groth, Britt-Sabina Petersen, Andre Franke, Wolfgang Lieb, Klaus Huse, Peter F Zipfel, Oliver Kurzai, Barbara Moepps, Peter Gierschik, Michael Bauer, André Scherag, Hans A Kestler, Matthias Platzer
Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. For its clinical course, host genetic factors are important and rare genomic variants are suspected to contribute. We sequenced the exomes of 59 Greek and 15 German patients with bacterial sepsis divided into two groups with extremely different disease courses. Variant analysis was focusing on rare deleterious single nucleotide variants (SNVs). We identified significant differences in the number of rare deleterious SNVs per patient between the ethnic groups...
September 14, 2016: EBioMedicine
https://www.readbyqxmd.com/read/27624097/differentiation-of-foodborne-bacteria-using-nir-hyperspectral-imaging-and-multivariate-data-analysis
#19
Terri-Lee Kammies, Marena Manley, Pieter A Gouws, Paul J Williams
The potential for near-infrared (NIR) hyperspectral imaging and multivariate data analysis to be used as a rapid non-destructive tool for detection and differentiation of bacteria was investigated. NIR hyperspectral images were collected of Bacillus cereus, Escherichia coli, Salmonella enteritidis, Staphylococcus aureus and Staphylococcus epidermidis grown on agar for 20 h at 37 °C. Principal component analysis (PCA) was applied to mean-centred data. Standard normal variate (SNV) correction and the Savitzky-Golay technique was applied (2nd derivative, 3rd-order polynomial; 25 point smoothing) to wavelengths in the range of 1103 to 2471 nm...
November 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27612449/a-hybrid-computational-strategy-to-address-wgs-variant-analysis-in-5000-samples
#20
Zhuoyi Huang, Navin Rustagi, Narayanan Veeraraghavan, Andrew Carroll, Richard Gibbs, Eric Boerwinkle, Manjunath Gorentla Venkata, Fuli Yu
BACKGROUND: The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies...
September 10, 2016: BMC Bioinformatics
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