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Whole genome alignment

Hassol Lim, Young-Mi Park, Jong-Keuk Lee, Hyun Taek Lim
OBJECTIVE: To present an efficient and successful application of a single-exome sequencing study in a family clinically diagnosed with X-linked retinitis pigmentosa. DESIGN: Exome sequencing study based on clinical examination data. PARTICIPANTS: An 8-year-old proband and his family. METHODS: The proband and his family members underwent comprehensive ophthalmologic examinations. Exome sequencing was undertaken in the proband using Agilent SureSelect Human All Exon Kit and Illumina HiSeq 2000 platform...
October 2016: Canadian Journal of Ophthalmology. Journal Canadien D'ophtalmologie
Zhangguo Chen, Katherine Gowan, Sonia M Leach, Sawanee S Viboolsittiseri, Ameet K Mishra, Tanya Kadoishi, Katrina Diener, Bifeng Gao, Kenneth Jones, Jing H Wang
BACKGROUND: Whole genome next generation sequencing (NGS) is increasingly employed to detect genomic rearrangements in cancer genomes, especially in lymphoid malignancies. We recently established a unique mouse model by specifically deleting a key non-homologous end-joining DNA repair gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in germinal center B cells. This mouse model spontaneously develops mature B cell lymphomas (termed G1XP lymphomas). RESULTS: Here, we attempt to employ whole genome NGS to identify novel structural rearrangements, in particular inter-chromosomal translocations (CTXs), in these G1XP lymphomas...
October 21, 2016: BMC Genomics
Michał Książkiewicz, Sandra Rychel, Matthew N Nelson, Katarzyna Wyrwa, Barbara Naganowska, Bogdan Wolko
BACKGROUND: The Arabidopsis FLOWERING LOCUS T (FT) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality. In legumes, FT evolved into three, functionally diversified clades, FTa, FTb and FTc. A milestone achievement in narrow-leafed lupin (Lupinus angustifolius L.) domestication was the loss of vernalization responsiveness at the Ku locus. Recently, one of two existing L...
October 21, 2016: BMC Genomics
Andrew P Morgan, John P Didion, Anthony G Doran, James M Holt, Leonard McMillan, Thomas M Keane, Fernando Pardo-Manuel de Villena
Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14X and 18X coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains...
October 7, 2016: G3: Genes—Genomes—Genetics
Kari Branham, Hiroko Matsui, Pooja Biswas, Aditya A Guru, Michael Hicks, John J Suk, He Li, David Jakubosky, Tao Long, Amalio Telenti, Naoki Narai, John R Heckenlively, Kelly A Frazar, Paul A Sieving, Radha Ayyagari
While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40-50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of inherited retinal degeneration (IRD) in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10...
October 7, 2016: Physiological Genomics
Olga V Popova, Kirill V Mikhailov, Mikhail A Nikitin, Maria D Logacheva, Aleksey A Penin, Maria S Muntyan, Olga S Kedrova, Nikolai B Petrov, Yuri V Panchin, Vladimir V Aleoshin
Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa...
2016: PloS One
Robert J Danaher, Derrick E Fouts, Agnes P Chan, Yongwook Choi, Jessica DePew, Jamison M McCorrison, Karen E Nelson, Chunmei Wang, Craig S Miller
Strain-specific factors contribute in significant but undefined ways to the variable incidence of herpes simplex virus (HSV) recrudescence. Studies that investigate these strain-specific factors are needed. Here, we used qPCR, in vitro assays, and genomic sequencing to identify important relationships between in vitro and clinical phenotypes of unique HSV-1 clinical isolates. Nine HSV-1 isolates from individuals displaying varying reactivation patterns were studied. Isolates associated with frequent recurrent herpes labialis (RHL) (1) displayed higher rates of viral shedding in the oral cavity than those associated with rare RHL and (2) tended to replicate more efficiently at 33 °C than 39 °C...
October 13, 2016: Journal of Neurovirology
Jiwoong Kim, Min Soo Kim, Andrew Y Koh, Yang Xie, Xiaowei Zhan
BACKGROUND: Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. RESULTS: Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline)...
October 10, 2016: BMC Bioinformatics
Shenglin Liu, Michael M Hansen
The Pairwise Sequentially Markovian Coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole genome data, we here use simulations to investigate its applicability to reference genome aligned RAD (Restriction site Associated DNA) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers...
October 8, 2016: Molecular Ecology Resources
Shulan Tian, Huihuang Yan, Michael Kalmbach, Susan L Slager
BACKGROUND: GATK Best Practices workflows are widely used in large-scale sequencing projects and recommend post-alignment processing before variant calling. Two key post-processing steps include the computationally intensive local realignment around known INDELs and base quality score recalibration (BQSR). Both have been shown to reduce erroneous calls; however, the findings are mainly supported by the analytical pipeline that incorporates BWA and GATK UnifiedGenotyper. It is not known whether there is any benefit of post-processing and to what extent the benefit might be for pipelines implementing other methods, especially given that both mappers and callers are typically updated...
October 3, 2016: BMC Bioinformatics
Patricia Morán Losada, Burkhard Tümmler
Genomic sequence diversity of a bacterial species mainly results from the frequency distribution of single nucleotide polymorphisms (SNPs). Here we report on a SNP-matrix based binary algorithm to determine the intra- or interclonal genomic diversity by the number of shared sequential SNPs, the so-called SNP synteny or haplotype. All SNP positions and the frequency and length distribution of haplotypes are determined from pairwise alignment of completely sequenced genomes. This metric is invariant regarding the reference genome chosen...
October 3, 2016: FEMS Microbiology Letters
Minenosuke Matsutani, Hideki Hirakawa, Eri Hiraoka, Gunjana Theeragool, Toshiharu Yakushi, Kazunobu Matsushita
Acetobacter pasteurianus SKU1108 is a typical thermotolerant acetic acid bacterium. In this study, the complete genome sequence of the SKU1108 strain was elucidated, and information on genomic modifications due to the thermal adaptation of SKU1108 was updated. In order to obtain a clearer understanding of the genetic background responsible for thermotolerance, the SKU1108 genome was compared with those of two closely related complete genome strains, thermotolerant A. pasteurianus 386B and mesophilic A. pasteurianus NBRC 3283...
September 24, 2016: Microbes and Environments
C J Anderson, W T Tay, A McGaughran, K Gordon, T K Walsh
Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region-specific lineages...
September 23, 2016: Molecular Ecology
Changwei Bi, Yiqing Xu, Qiaolin Ye, Tongming Yin, Ning Ye
WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow...
2016: PeerJ
Michael R McKain, Ryan H Hartsock, Molly M Wohl, Elizabeth A Kellogg
MOTIVATION: Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation,alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. RESULTS: Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention...
September 14, 2016: Bioinformatics
Amit Kumar Gupta, Karambir Kaur, Akanksha Rajput, Sandeep Kumar Dhanda, Manika Sehgal, Md Shoaib Khan, Isha Monga, Showkat Ahmad Dar, Sandeep Singh, Gandharva Nagpal, Salman Sadullah Usmani, Anamika Thakur, Gazaldeep Kaur, Shivangi Sharma, Aman Bhardwaj, Abid Qureshi, Gajendra Pal Singh Raghava, Manoj Kumar
Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (, dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content...
2016: Scientific Reports
Zohreh Moradi, Mohsen Mehrvar, Ehsan Nazifi, Mohammad Zakiaghl
Iranian johnsongrass mosaic virus (IJMV) is one of the most prevalent viruses causing maize mosaic disease in Iran. An IJMV isolate, Maz-Bah, was obtained from the maize showing mosaic symptoms in Mazandaran, north of Iran. The complete genomic sequence of Maz-Bah is 9544 nucleotides, excluding the poly(A) tail. It contains one single open reading frame of 9165 nucleotides and encodes a large polyprotein of 3054 amino acids, flanked by a 5'-untranslated region (UTR) of 143 nucleotides and a 3'-UTR of 236 nucleotides...
September 8, 2016: Virus Genes
Moise C Ngwa, Thomas Masalla, Seraphine Esemu, Foche Francis Fumoloh, Ian Kracalik, Eleonora Cella, Meer Taifur Alam, Jane-Francis Akoachere, Song Liang, Marco Salemi, J Glenn Morris, Afsar Ali, Lucy M Ndip
INTRODUCTION: During the cholera outbreak from 2010 to 2011 in Cameroon, 33,192 cases with 1,440 deaths (case fatality ratio 4.34%) were reported to the World Health Organization. Of these, the South West Region reported 3,120 clinical cases. This region is in the Equatorial Monsoon climatic subzone of Cameroon, close to the coast, raising questions as to whether cases were linked with development of environmental reservoirs. METHODS: In an investigation conducted by the Laboratory for Emerging Infectious Diseases, University of Buea, toxigenic V...
2016: PLoS Currents
Steven R Eichten, Tim Stuart, Akanksha Srivastava, Ryan Lister, Justin O Borevitz
DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines...
September 9, 2016: Genome Research
Steve Laurie, Marcos Fernandez-Callejo, Santiago Marco-Sola, Jean-Remi Trotta, Jordi Camps, Alejandro Chacón, Antonio Espinosa, Marta Gut, Ivo Gut, Simon Heath, Sergi Beltran
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample...
September 8, 2016: Human Mutation
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