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Ernst Joachim Houtgast, Vlad-Mihai Sima, Koen Bertels, Zaid Al-Ars
We present our work on hardware accelerated genomics pipelines, using either FPGAs or GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read mapping. The mapping stage can take up to 40% of overall processing time for genomics pipelines. Our implementation offloads the Seed Extension function, one of the main BWA-MEM computational functions, onto an accelerator. Sequencers typically output reads with a length of 150 base pairs. However, read length is expected to increase in the near future...
April 12, 2018: Computational Biology and Chemistry
Daichi Shigemizu, Fuyuki Miya, Shintaro Akiyama, Shujiro Okuda, Keith A Boroevich, Akihiro Fujimoto, Hidewaki Nakagawa, Kouichi Ozaki, Shumpei Niida, Yonehiro Kanemura, Nobuhiko Okamoto, Shinji Saitoh, Mitsuhiro Kato, Mami Yamasaki, Tatsuo Matsunaga, Hideki Mutai, Kenjiro Kosaki, Tatsuhiko Tsunoda
Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads...
April 4, 2018: Scientific Reports
Saeed Amini Komijani
Importance of 2'-deoxyguanosine-uridine mispair as the most occurring mismatch in transcriptional studies of RNAs from DNAs is multiplied when 5-halo-substituted uridine species cause to serious increase in probability of its occurrence. Many studies relate this higher probability to existence of possible tautomeric and ionic forms of its constituent bases. According to these statements, relative populations of mismatches between 5-fluorouridine and both keto and enol forms of 2'-deoxyguanosine are computed by using conformational search...
April 2, 2018: Journal of Physical Chemistry. B
Samira Asgharzade, Mohammad Amin Tabatabaiefar, Javad Mohammadi-Asl, Morteza Hashemzadeh Chaleshtori
BACKGROUND: Recent studies have confirmed the utility of targeted next-generation sequencing (NGS), providing a remarkable opportunity to find variants in known disease genes, especially in genetically heterogeneous disorders such as hearing loss (HL). METHODS: After excluding mutations in the most common autosomal recessive non-syndromic HL (ARNSHL) genes via Sanger sequencing and genetic linkage analysis, we performed NGS in the proband an Iranian family with ARNSHL...
May 2018: International Journal of Pediatric Otorhinolaryngology
Nasrollah Saleh-Gohari, Kolsoum Saeidi, Roya Zeighaminejad
AIMS: Fucosidosis is a rare autosomal recessive lysosomal storage disorder caused by α-L-fucosidase deficiency as a result of FUCA1 gene mutations. Here, we studied clinical features and the molecular basis of fucosidosis in a family from Iran, including two probands and nine family members. METHODS: DNA sample of two probands were screened for gene defects using a next generation sequencing technique. The sequencing processes were performed on an Illumina Hiseq 4000 platform...
March 27, 2018: Journal of Clinical Pathology
Vanessa Rew, Piers Mook, Suzan Trienekens, Kate S Baker, Timothy J Dallman, Claire Jenkins, Paul D Crook, Nicholas R Thomson
In December 2013, Public Health England (PHE) observed an increase in the number of cases of Shigella sonnei linked to the Orthodox Jewish Community (OJC). Ultimately, 52 cases of S. sonnei phage type (PT) P and PT7 were notified between November 2013 and July 2014. Whole-genome sequencing (WGS) was performed on a HiSeq 2500 platform (Illumina) on isolates of S. sonnei submitted to PHE during the investigation. Quality trimmed sequence reads were mapped to a reference genome using BWA-MEM, and single-nucleotide polymorphisms (SNPs) were identified using GATK2...
March 27, 2018: Microbial Genomics
Xiwei Sun, Yi Han, Liyuan Zhou, Enguo Chen, Bingjian Lu, Yong Liu, Xiaoqing Pan, Allen W Cowley, Mingyu Liang, Qingbiao Wu, Yan Lu, Pengyuan Liu
Motivation: The rapid development of next-generation sequencing technology provides an opportunity to study genome-wide DNA methylation at single-base resolution. However, depletion of unmethylated cytosines brings challenges for aligning bisulfite-converted sequencing reads to a large reference. Software tools for aligning methylation reads have not yet been comprehensively evaluated, especially for the widely used reduced representation bisulfite sequencing (RRBS) that involves enrichment for CpG islands (CGIs)...
March 22, 2018: Bioinformatics
Hojun Lee, Ki-Wook Lee, Taeseob Lee, Donghyun Park, Jongsuk Chung, Chung Lee, Woong-Yang Park, Dae-Soon Son
In addition to the rapid advancement in Next-Generation Sequencing (NGS) technology, clinical panel sequencing is being used increasingly in clinical studies and tests. However, tools that are used in NGS data analysis have not been comparatively evaluated in performance for panel sequencing. This study aimed to evaluate the tools used in the alignment process, the first procedure in bioinformatics analysis, by comparing tools that have been widely used with ones that have been introduced recently. With the accumulated panel sequencing data, detected variant lists were cataloged and inserted into simulated reads produced from the reference genome (h19)...
2018: Genes & Genomics
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
C McCall, I 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 antibiotic resistance genes using next generation sequencing...
March 2018: 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...
March 15, 2018: 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
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