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Brittney N Keel, Warren M Snelling
Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Efficient alignment of the reads onto the reference genome with high accuracy is very important because it determines the global quality of downstream analyses. In this study, we evaluate the performance of three Burrows-Wheeler transform-based mappers, BWA, Bowtie2, and HISAT2, in the context of paired-end Illumina whole-genome sequencing of livestock, using simulated sequence data sets with varying sequence read lengths, insert sizes, and levels of genomic coverage, as well as five real data sets...
2018: Frontiers in Genetics
Anne Brédart, Jean-Luc Kop, Antonis C Antoniou, Alex P Cunningham, Antoine De Pauw, Marc Tischkowitz, Hans Ehrencrona, Marjanka K Schmidt, Sylvie Dolbeault, Kerstin Rhiem, Douglas F Easton, Peter Devilee, Dominique Stoppa-Lyonnet, Rita Schmutlzer
The BOADICEA breast cancer (BC) risk assessment model and its associated Web Application v3 (BWA) tool are being extended to incorporate additional genetic and non-genetic BC risk factors. From an online survey through the BOADICEA website and UK, Dutch, French and Swedish national genetic societies, we explored the relationships between the usage frequencies of the BWA and six other common BC risk assessment tools and respondents' perceived importance of BC risk factors. Respondents (N = 443) varied in age, country and clinical seniority but comprised mainly genetics health professionals (82%) and BWA users (93%)...
March 5, 2018: Journal of Community Genetics
Deborah Wilson, Gayle Dolan, Heather Aird, Shirley Sorrell, Timothy J Dallman, Claire Jenkins, Lucy Robertson, Russell Gorton
Fifteen cases of Shiga toxin-producing Escherichia coli (STEC) O157 infection were associated with the consumption of contaminated food from two related butchers' premises in the north-east of England. Ten cases were admitted to hospital and seven cases developed haemolytic uraemic syndrome. A case control study found a statistically significant association with the purchase of raw and/or ready-to-eat (RTE) food supplied by the implicated butchers' shops. Isolates of STEC O157 were detected in two raw lamb burgers taken from one of the butchers' premises...
February 28, 2018: Microbial Genomics
Xuelin Wang, Feng Cheng, Dekai Rohlsen, Changwei Bi, Chunyan Wang, Yiqing Xu, Suyun Wei, Qiaolin Ye, Tongming Yin, Ning Ye
Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants...
2018: Horticulture Research
Camille McCall, Irene Xagoraraki
We aim to compare the performance of Bowtie2, BWA-MEM, BLASTN, and BLASTX when aligning bacterial metagenomes against the Comprehensive Antibiotic Resistance Database (CARD). Simulated reads were used to evaluate the performance of each aligner under the following four performance criteria: correctly mapped, false positives, multi-reads, and partials. The optimal alignment approach was applied to samples from two wastewater treatment plants to detect ARGs using next generation sequencing. BLASTN mapped with greater accuracy among the four sequence alignment approaches considered followed by Bowtie2...
December 30, 2017: Letters in Applied Microbiology
Henning Krampe, Anna-Lena Salz, Léonie F Kerper, Alexander Krannich, Tatjana Schnell, Klaus-Dieter Wernecke, Claudia D Spies
BACKGROUND: Readiness to change is a pivotal construct for psychotherapy research and a major target of motivational interventions. Our primary objective was to examine whether pre-treatment readiness to change moderated therapy effects of Bridging Intervention in Anesthesiology (BRIA), an innovative psychotherapy approach for surgical patients. This stepped care program aims at motivating and supporting surgical patients with mental disorders to engage in psychosocial mental health care...
December 29, 2017: BMC Psychiatry
Zeeshan Ahmed, Duygu Ucar
Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors...
2017: PeerJ
Kelly M Robinson, Aziah S Hawkins, Ivette Santana-Cruz, Ricky S Adkins, Amol C Shetty, Sushma Nagaraj, Lisa Sadzewicz, Luke J Tallon, David A Rasko, Claire M Fraser, Anup Mahurkar, Joana C Silva, Julie C Dunning Hotopp
As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i...
September 2017: Microbial Genomics
Altti Ilari Maarala, Zurab Bzhalava, Joakim Dillner, Keijo Heljanko, Davit Bzhalava
Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments...
November 2, 2017: Bioinformatics
K Yu Tsukanov, A Yu Krasnenko, D A Plakhina, D O Korostin, A V Churov, O S Druzhilovskaya, D V Rebrikov, V V Ilinsky
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
Xuning Wang, Charles Tilford, Isaac Neuhaus, Gabe Mintier, Qi Guo, John N Feder, Stefan Kirov
Summary: The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view...
December 1, 2017: Bioinformatics
Ragaa T Darwish, Manal H Abdel-Aziz, Abdel-Aziz M El Nekiedy, Zahraa K Sobh
BACKGROUND: In forensic sciences to determine one's sex is quite important during the identity defining stage. The reliability of sex determination depends on the completeness of the remains and the degree of sexual dimorphism inherent in the population. Computed Tomography is the imaging modality of choice for two- and three-dimensional documentation and analysis of many autopsy findings. OBJECTIVE: The aim of the present work was to assess the reliability of Three-dimensional Multislice Computed Tomography (3D MSCT) to determine sexual dimorphism from certain chest measurements; sternum and fourth rib using the 3D MSCT and to develop equations for sex determination from these bones among adult Egyptians sample...
November 2017: Journal of Forensic and Legal Medicine
Xueqin Wang, Xiaying Ye, Lei Zhao, Dezhu Li, Zhenhua Guo, Huifu Zhuang
The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution...
September 14, 2017: Scientific Reports
E H Ernst, M L Grøndahl, S Grund, K Hardy, A Heuck, L Sunde, S Franks, C Y Andersen, P Villesen, K Lykke-Hartmann
STUDY QUESTION: Do specific transcriptome dynamics in human oocytes from primordial and primary follicles identify novel pathways in oocyte activation? SUMMARY ANSWER: The transcriptomic profiles in oocytes from primordial and primary follicles, respectively, revealed several new canonical pathways as putative mediators of oocyte dormancy and activation. WHAT IS KNOWN ALREADY: Cellular signaling pathways including PI3K/AKT and AKT/mTOR as well as TGF-β and IGF signaling are known to regulate the primordial-to-primary transition in mammalian follicle development...
August 1, 2017: Human Reproduction
Anne Brédart, Jean-Luc Kop, Antonis C Antoniou, Alex P Cunningham, Antoine De Pauw, Marc Tischkowitz, Hans Ehrencrona, Sylvie Dolbeault, Léonore Robieux, Kerstin Rhiem, Douglas F Easton, Peter Devilee, Dominique Stoppa-Lyonnet, Rita Schmutlzer
The 'BOADICEA' Web Application (BWA) used to assess breast cancer risk, is currently being further developed, to integrate additional genetic and non-genetic factors. We surveyed clinicians' perceived acceptability of the existing BWA v3. An online survey was conducted through the BOADICEA website, and the British, Dutch, French and Swedish genetics societies. Cross-sectional data from 443 participants who provided at least 50% responses were analysed. Respondents varied in age and, clinical seniority, but mainly comprised women (77%) and genetics professionals (82%)...
June 16, 2017: Familial Cancer
Xiangqun Zheng-Bradley, Ian Streeter, Susan Fairley, David Richardson, Laura Clarke, Paul Flicek
The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies...
July 1, 2017: GigaScience
N K T Hlaing, R A Mitrani, S T Aung, W W Phyo, M Serper, A M M Kyaw, A H Bwa, K M Win, K R Reddy
This open-label, clinical experience investigated the safety and efficacy of direct-acting antiviral (DAA) hepatitis C virus (HCV) therapy in Myanmar; 344 patients completed treatment between June 2015 and May 2016. Patients with HCV genotypes 1-4 and 6 received one of four treatments: (i) Peg-interferon (PEG-IFN)+sofosbuvir (SOF)+ribavirin (RBV) for 12 weeks, (ii) SOF+RBV for 24 weeks, (iii) ledipasvir (LDV)+SOF for 12 weeks or (iv) daclatasvir (DCV)+SOF+RBV for 12 or 24 weeks. Genotype 3 was most common (n=133, 38...
November 2017: Journal of Viral Hepatitis
Shulan Tian, Huihuang Yan, Eric W Klee, Michael Kalmbach, Susan L Slager
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data...
April 11, 2017: Briefings in Bioinformatics
Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes...
July 2017: Genomics
M H Elsensohn, N Leblay, S Dimassi, A Campan-Fournier, A Labalme, F Roucher-Boulez, D Sanlaville, G Lesca, C Bardel, P Roy
BACKGROUND: Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients...
March 1, 2017: BMC Bioinformatics
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