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"Cost genomic"

Shun Sawatsubashi, Yudai Joko, Seiji Fukumoto, Toshio Matsumoto, Shigeo S Sugano
CRISPR/Cas9-based genome editing has dramatically accelerated genome engineering. An important aspect of genome engineering is efficient knock-in technology. For improved knock-in efficiency, the non-homologous end joining (NHEJ) repair pathway has been used over the homology-dependent repair pathway, but there remains a need to reduce the complexity of the preparation of donor vectors. We developed the versatile NHEJ-based knock-in module for genome editing (VIKING). Using the consensus sequence of the time-honored pUC vector to cut donor vectors, any vector with a pUC backbone could be used as the donor vector without customization...
January 12, 2018: Scientific Reports
Erin C Bush, Forest Ray, Mariano J Alvarez, Ronald Realubit, Hai Li, Charles Karan, Andrea Califano, Peter A Sims
Pharmacological and functional genomic screens play an essential role in the discovery and characterization of therapeutic targets and associated pharmacological inhibitors. Although these screens affect thousands of gene products, the typical readout is based on low complexity rather than genome-wide assays. To address this limitation, we introduce pooled library amplification for transcriptome expression (PLATE-Seq), a low-cost, genome-wide mRNA profiling methodology specifically designed to complement high-throughput screening assays...
July 24, 2017: Nature Communications
Danillo O Alvarenga, Marli F Fiore, Alessandro M Varani
Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium...
2017: Frontiers in Microbiology
Mitsuyuki Matsumoto, Noah M Walton, Hiroshi Yamada, Yuji Kondo, Gerard J Marek, Katsunori Tajinda
Failures of investigational new drugs (INDs) for schizophrenia have left huge unmet medical needs for patients. Given the recent lackluster results, it is imperative that new drug discovery approaches (and resultant drug candidates) target pathophysiological alterations that are shared in specific, stratified patient populations that are selected based on pre-identified biological signatures. One path to implementing this paradigm is achievable by leveraging recent advances in genetic information and technologies...
July 2017: Expert Opinion on Drug Discovery
Xiumei Jiang, Lutao Du, Weili Duan, Rui Wang, Keqiang Yan, Lili Wang, Juan Li, Guixi Zheng, Xin Zhang, Yongmei Yang, Chuanxin Wang
Noninvasive biomarkers for predicting the risk of muscle-invasive bladder cancer (MIBC) may expedite appropriate therapy and reduce morbidity and cost. Genome-wide miRNA analysis by Miseq sequencing followed by two phases of reverse transcription quantitative real-time PCR (RT-qPCR) assays were performed on serum from 207 MIBC patients, 285 nonmuscle-invasive bladder cancer (NMIBC) patients and 193 controls. A four-miRNA panel (miR-422a-3p, miR-486-3p, miR-103a-3p and miR-27a-3p) was developed for MIBC prediction with an area under the receiver operating characteristic curve (AUC) of 0...
June 14, 2016: Oncotarget
Simon Uribe-Convers, Matthew L Settles, David C Tank
Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array)...
2016: PloS One
Uwe Baier, Timo Beller, Enno Ohlebusch
MOTIVATION: Low-cost genome sequencing gives unprecedented complete information about the genetic structure of populations, and a population graph captures the variations between many individuals of a population. Recently, Marcus et al. proposed to use a compressed de Bruijn graph for representing an entire population of genomes. They devised an O(n log g) time algorithm called splitMEM that constructs this graph directly (i.e. without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome...
February 15, 2016: Bioinformatics
Huaan Yang, Jianbo Jian, Xuan Li, Daniel Renshaw, Jonathan Clements, Mark W Sweetingham, Cong Tan, Chengdao Li
BACKGROUND: Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding...
2015: BMC Genomics
Andrew D Hellicar, Ashfaqur Rahman, Daniel V Smith, John M Henshall
BACKGROUND: Despite ongoing reduction in genotyping costs, genomic studies involving large numbers of species with low economic value (such as Black Tiger prawns) remain cost prohibitive. In this scenario DNA pooling is an attractive option to reduce genotyping costs. However, genotyping of pooled samples comprising DNA from many individuals is challenging due to the presence of errors that exceed the allele frequency quantisation size and therefore cannot be simply corrected by clustering techniques...
July 9, 2015: BMC Bioinformatics
David M Thomas, Paul A James, Mandy L Ballinger
The study of human genetics has provided substantial insight into cancer biology. With an increase in sequencing capacity and a reduction in sequencing costs, genomics will probably transform clinical cancer genetics. A heritable basis for many cancers is accepted, but so far less than half the genetic drivers have been identified. Genomics will increasingly be applied to populations irrespective of family history, which will change the framework of phenotype-directed genetic testing. Panel testing and whole genome sequencing will identify novel, polygenic, and de-novo determinants of cancer risk, often with lower penetrance, which will challenge present binary clinical classification systems and management algorithms...
June 2015: Lancet Oncology
Shuang Wang, Noman Mohammed, Rui Chen
Advanced sequencing techniques make large genome data available at an unprecedented speed and reduced cost. Genome data sharing has the potential to facilitate significant medical breakthroughs. However, privacy concerns have impeded efficient genome data sharing. In this paper, we present a novel approach for disseminating genomic data while satisfying differential privacy. The proposed algorithm splits raw genome sequences into blocks, subdivides the blocks in a top-down fashion, and finally adds noise to counts to preserve privacy...
2014: BMC Medical Informatics and Decision Making
Daniel W Belsky, Salomon Israel
The sequencing of the human genome and the advent of low-cost genome-wide assays that generate millions of observations of individual genomes in a matter of hours constitute a disruptive innovation for social science. Many public use social science datasets have or will soon add genome-wide genetic data. With these new data come technical challenges, but also new possibilities. Among these, the lowest-hanging fruit and the most potentially disruptive to existing research programs is the ability to measure previously invisible contours of health and disease risk within populations...
2014: Biodemography and Social Biology
Christian Schlötterer, Raymond Tobler, Robert Kofler, Viola Nolte
The analysis of polymorphism data is becoming increasingly important as a complementary tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs, genomic sequencing of individuals at the population scale is still restricted to a few model species. Whole-genome sequencing of pools of individuals (Pool-seq) provides a cost-effective alternative to sequencing individuals separately. With the availability of custom-tailored software tools, Pool-seq is being increasingly used for population genomic research on both model and non-model organisms...
November 2014: Nature Reviews. Genetics
Sanaa M Kamal
Hepatitis C virus (HCV) has emerged as a major viral pandemic over the past two decades, infecting 170 million individuals, which equates to approximately 3% of the world's population. The prevalence of HCV varies according to geographic region, being highest in developing countries such as Egypt. HCV has a high tendency to induce chronic progressive liver damage in the form of hepatic fibrosis, cirrhosis, or liver cancer. To date, there is no vaccine against HCV infection. Combination therapy comprising PEGylated interferon-alpha and ribavirin has been the standard of care for patients with chronic hepatitis C for more than a decade...
2014: Hepatic Medicine: Evidence and Research
David Laehnemann, Rafael Peña-Miller, Philip Rosenstiel, Robert Beardmore, Gunther Jansen, Hinrich Schulenburg
Evolutionary adaptation can be extremely fast, especially in response to high selection intensities. A prime example is the surge of antibiotic resistance in bacteria. The genomic underpinnings of such rapid changes may provide information on the genetic processes that enhance fast responses and the particular trait functions under selection. Here, we use experimentally evolved Escherichia coli for a detailed dissection of the genomics of rapid antibiotic resistance evolution. Our new analyses demonstrate that amplification of a sequence region containing several known antibiotic resistance genes represents a fast genomic response mechanism under high antibiotic stress, here exerted by drug combination...
May 20, 2014: Genome Biology and Evolution
Xiangyu Fan, Longxiang Xie, Wu Li, Jianping Xie
BACKGROUND: Prophages, integral components of many bacterial genomes, play significant roles in cognate host bacteria, such as virulence, toxin biosynthesis and secretion, fitness cost, genomic variations, and evolution. Many prophages and prophage-like elements present in sequenced bacterial genomes, such as Bifidobacteria, Lactococcus and Streptococcus, have been described. However, information for the prophage of Mycobacterium remains poorly defined. RESULTS: In this study, based on the search of the complete genome database from GenBank, the Whole Genome Shotgun (WGS) databases, and some published literatures, thirty-three prophages were described in detail...
2014: BMC Genomics
Luigi Faino, Bart P H J Thomma
The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model organisms. Here, we show that a high-quality draft genome of a eukaryote can be obtained at relatively low cost by exploiting a hybrid combination of sequencing strategies.
May 2014: Trends in Plant Science
Jørgen Odegård, Theo H E Meuwissen
BACKGROUND: Genomic selection methods require dense and widespread genotyping data, posing a particular challenge if both sexes are subject to intense selection (e.g., aquaculture species). This study focuses on alternative low-cost genomic selection methods (IBD-GS) that use selective genotyping with sparse marker panels to estimate identity-by-descent relationships through linkage analysis. Our aim was to evaluate the potential of these methods in selection programs for continuous traits measured on sibs of selection candidates in a typical aquaculture breeding population...
2014: Genetics, Selection, Evolution: GSE
Bin Han, Xuehui Huang
Rice, which has a modest genome size, is a wonderful model crop that has been comprehensively studied in functional genomics. With vast germplasm resources and reduced sequencing cost, genome-wide association study (GWAS) has been feasible to explore the allelic variation underlying agronomic traits in rice. In this review, we firstly summarize the work on constructing GWAS platforms in human genetics and in Arabidopsis and maize, from which we have a lot to learn. We then discuss the sequencing strategies and experimental designs for GWAS of agronomic traits in rice, and the perspective and challenges coupled with GWAS work are further addressed...
May 2013: Current Opinion in Plant Biology
Mark S Boguski, Robert M Boguski, Michele R Berman
There is an urgent need for effective genomics education for healthcare professionals. Recent analysis of an experimental genomics curriculum showed that medical students' examinations of their own genotypes provide a valuable learning experience. Such experiential learning has a long tradition in medical education and its application to genomics is enabled by increasingly powerful and decreasingly costly genome science and technology. Personal genotyping is an important option to consider when designing educational programs for healthcare professionals...
2013: Genome Medicine
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