共查询到20条相似文献,搜索用时 0 毫秒
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Hattori M 《Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme》2000,45(12):1978-1985
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Thierry Voet Parveen Kumar Peter Van Loo Susanna L. Cooke John Marshall Meng-Lay Lin Masoud Zamani Esteki Niels Van der Aa Ligia Mateiu David J. McBride Graham R. Bignell Stuart McLaren Jon Teague Adam Butler Keiran Raine Lucy A. Stebbings Michael A. Quail Thomas D’Hooghe Yves Moreau P. Andrew Futreal Michael R. Stratton Joris R. Vermeesch Peter J. Campbell 《Nucleic acids research》2013,41(12):6119-6138
The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis. 相似文献
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Toward nanoscale genome sequencing 总被引:2,自引:0,他引:2
This article reports on the state-of-the-art technologies that sequence DNA using miniaturized devices. The article considers the miniaturization of existing technologies for sequencing DNA and the opportunities for cost reduction that 'on-chip' devices can deliver. The ability to construct nano-scale structures and perform measurements using novel nano-scale effects has provided new opportunities to identify nucleotides directly using physical, and not chemical, methods. The challenges that these technologies need to overcome to provide a US$1000-genome sequencing technology are also presented. 相似文献
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《Fungal Biology Reviews》2008,22(1):1-5
To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions. 相似文献
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Advances in plant genome sequencing 总被引:1,自引:0,他引:1
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The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human
and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers
based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern
bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost
of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the
HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation
coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome
wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection
of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of
mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation
DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule
Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS
platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research. 相似文献
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The year 1997 saw the publication of the complete nucleotide sequence of Helicobacter pylori and Escherichia coli. It is conceivable that the complete nucleotide sequence for all the major human bacterial pathogens will be available by the end of the century. Database alignments have been used to ascribe the putative functions of open reading frames in the sequenced isolates and to define the differences between bacterial species at the nucleotide level. The most striking finding from all genome projects has been the high proportion of open reading frames that have no known function. Experimental data demonstrating the utility of the genome sequencing projects are only just beginning to emerge. 相似文献
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We consider the general problem of constructing a physical map of a genome by welding islands of overlapping clones. Both
distribution of clone length and non-uniform probability of overlap detection are taken into account, the latter restricted
to the Markov case in which only the location of the end of the developing island is required. Exact results for the distribution
of island length are obtained in the special cases of fixed clone length or rigid overlap criterion, and mean and variance
for the general situation. Determination of ocean length distribution permits island number and contig number distributions
to be found as well.
Received: 21 December 1998 相似文献
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Carlton J 《Trends in parasitology》2003,19(5):227-231
With the successful completion of the project to sequence the Plasmodium falciparum genome, researchers are now turning their attention to other malaria parasite species. Here, an update on the Plasmodium vivax genome sequencing project is presented, as part of the Trends in Parasitology series of reviews expanding on various aspects of P. vivax research. 相似文献
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New directions of post-rice genome sequencing 总被引:1,自引:0,他引:1
Matsuoka M 《Plant & cell physiology》2005,46(1):1-2
Rice (Oryza sativa L.) is one of the most important staple foodsand it has been estimated that 50% of the human population dependson it as the main source of nutrition. It is particularly importantfor people living in the monsoon areas of Asia, where it hasa long history of cultivation. On April 2002, two groups, Syngentaand the Beijing Genome Institute, reported draft sequences ofjaponica and indica varieties, respectively (Goff et al. 2002,Yu et al. 2002) and, in December of the 相似文献
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Cryptococcus neoformans is a basidiomycete that can cause life-threatening meningoencephalitis in patients with and without impaired immune function.
Cryptococcosis is usually an opportunistic infection in patients with compromised immunity as a consequence of HIV-1 infection,
steroid administration, cancer chemotherapy, sarcoidosis, diabetes, or inherited immune system defects. This pathogenic yeast
has a defined sexual cycle, which allows classical genetic analysis. Molecular biology approaches, including transformation
and gene disruption by homologous recombination, and animal models for studies of virulence are both well developed. Recently
an international consortium convened to begin the C. neoformans genome sequencing project, and we review here background and arguments for this project. We also discuss the importance of
this project to the biology and virulence of this organism in particular, and to virulence in general.
This revised version was published online in June 2006 with corrections to the Cover Date. 相似文献
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Aileen E Allsop 《Current opinion in biotechnology》1998,9(6):637-642
The availability of bacterial genome sequence information has opened up many new strategies for antibacterial drug hunting. There are obvious benefits for the idetification and evaluation of new drug targets, but genomic-based technology is also beginning to provide new tools for the downstream, preclinical, optimisation of compounds. The greatest benefit from these new approaches lies in the ability to examine the entire genome (or several genomes) simultaneously and in total. In this way, one potential target can be evaluated against another, and either the total effects of functional impairment can be established or the effects of a compound can be compared across species. 相似文献
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Dawes H 《Current biology : CB》2002,12(16):R541-R543
GENOMES: With the DNA sequencing of most key model organisms finished or well on the way, one genomics institute is filling an important niche, using novel criteria to take on species from organisms that occupy a unique place in the evolutionary tree to others that have an ability to digest explosives. 相似文献
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Burr B 《The Plant cell》2002,14(3):521-523
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Plastid sequencing is an essential tool in the study of plant evolution. This high‐copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low‐cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation‐sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short‐range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants. 相似文献
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Bedell JA Budiman MA Nunberg A Citek RW Robbins D Jones J Flick E Rholfing T Fries J Bradford K McMenamy J Smith M Holeman H Roe BA Wiley G Korf IF Rabinowicz PD Lakey N McCombie WR Jeddeloh JA Martienssen RA 《PLoS biology》2005,3(1):e13
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《Trends in parasitology》2021,37(9):803-814