Abstract：
BACKGROUND:Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Next Generation Sequencing (NGS) or enzymatic digestion, while broadly used in the genome editing field, has critical limitations for detecting and quantifying structural variants such as large deletions (greater than approximately 100 base pairs), inversions, and translocations. RESULTS:To overcome these limitations, we have developed a Uni-Directional Targeted Sequencing methodology, UDiTaS, that is quantitative, removes biases associated with variable-length PCR amplification, and can measure structural changes in addition to small insertion and deletion events (indels), all in a single reaction. We have applied UDiTaS to a variety of samples, including those treated with a clinically relevant pair of S. aureus Cas9 single guide RNAs (sgRNAs) targeting CEP290, and a pair of S. pyogenes Cas9 sgRNAs at T-cell relevant loci. In both cases, we have simultaneously measured small and large edits, including inversions and translocations, exemplifying UDiTaS as a valuable tool for the analysis of genome editing outcomes. CONCLUSIONS:UDiTaS is a robust and streamlined sequencing method useful for measuring small indels as well as structural rearrangements, like translocations, in a single reaction. UDiTaS is especially useful for pre-clinical and clinical application of gene editing to measure on- and off-target editing, large and small.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Giannoukos G,Ciulla DM,Marco E,Abdulkerim HS,Barrera LA,Bothmer A,Dhanapal V,Gloskowski SW,Jayaram H,Maeder ML,Skor MN,Wang T,Myer VE,Wilson CJdoi
10.1186/s12864-018-4561-9subject
Has Abstractpub_date
2018-03-21 00:00:00pages
212issue
1issn
1471-2164pii
10.1186/s12864-018-4561-9journal_volume
19pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract：BACKGROUND:Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-019-5467-x
更新日期：2019-04-04 00:00:00
abstract：BACKGROUND:Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. RESULTS:We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-11-454
更新日期：2010-07-28 00:00:00
abstract：BACKGROUND:The trypanosomatids Leishmania major, Trypanosoma brucei and Trypanosoma cruzi cause some of the most debilitating diseases of humankind: cutaneous leishmaniasis, African sleeping sickness, and Chagas disease. These protozoa possess complex life cycles that involve development in mammalian and insect hosts, ...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-6-127
更新日期：2005-09-15 00:00:00
abstract：BACKGROUND:Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on com...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-13-606
更新日期：2012-11-09 00:00:00
abstract：BACKGROUND:Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis w...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-018-5109-8
更新日期：2018-09-26 00:00:00
abstract：BACKGROUND:The pathogenesis-related (PR) group of proteins are operationally defined as polypeptides that increase in concentration in plant tissues upon contact with a pathogen. To date, 17 classes of highly divergent proteins have been described that act through multiple mechanisms of pathogen resistance. Characteriz...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-016-2693-3
更新日期：2016-05-17 00:00:00
abstract：UNLABELLED:Little is known, either experimentally or computationally, about the genomic sequence features that regulate malaria genes. A sequence conservation analysis of the malaria species P. falciparum, P. berghei, P. yoelii, and P. chabaudi could significantly advance knowledge of malaria gene regulation. RESULTS:...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-8-372
更新日期：2007-10-15 00:00:00
abstract：BACKGROUND:Association mapping approaches are dependent upon discovery and validation of single nucleotide polymorphisms (SNPs). To further association studies in Anopheles gambiae we conducted a major resequencing programme, primarily targeting regions within or close to candidate genes for insecticide resistance. RE...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-10-320
更新日期：2009-07-16 00:00:00
abstract：BACKGROUND:Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern ...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-9-399
更新日期：2008-08-27 00:00:00
abstract：BACKGROUND:The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploid wheat (Triticum aestivum L.). Future breeding efforts to enhance yield potential and climate re...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-019-5645-x
更新日期：2019-04-10 00:00:00
abstract：BACKGROUND:Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only t...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-11-260
更新日期：2010-04-22 00:00:00
abstract：BACKGROUND:Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD analyses require samples to be randomly collected, which, however, are usually ignored and thus rais...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-11-328
更新日期：2010-05-26 00:00:00
abstract：BACKGROUND:Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous involvement of multiple genes. Rothman's sufficient-cause model, which is well known in epidemiology, pro...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-14-497
更新日期：2013-07-23 00:00:00
abstract：BACKGROUND:One challenge of systems biology is the integration of new data into the preexisting, and then re-interpretation of the integrated data. Here we use readily available metaanalysis computational methods to integrate new data on the transcriptomic effects of EGF in primary human epidermal keratinocytes with pr...
journal_title：BMC genomics
pub_type： 杂志文章,meta分析
doi：10.1186/1471-2164-14-85
更新日期：2013-02-08 00:00:00
abstract：BACKGROUND:Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to ...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-020-06908-0
更新日期：2020-07-29 00:00:00
abstract：BACKGROUND:Human leukocyte antigen (HLA)-B27 is strongly associated with the development of reactive arthritis (ReA) in humans after salmonellosis. Human monocytic U937 cells transfected with HLA-B27 are less able to eliminate intracellular Salmonella enterica serovar Enteritidis than those transfected with control HLA...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-11-456
更新日期：2010-07-30 00:00:00
abstract：BACKGROUND:Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to c...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-016-2471-2
更新日期：2016-02-25 00:00:00
abstract：BACKGROUND:Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001. RESULTS:We did not find a significant difference between miRNA signature of both groups...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-13-379
更新日期：2012-08-07 00:00:00
abstract：BACKGROUND:The transcriptome of the fruit pulp of the sweet orange variety Anliu (WT) and that of its red fleshed mutant Hong Anliu (MT) were compared to understand the dynamics and differential expression of genes expressed during fruit development and ripening. RESULTS:The transcriptomes of WT and MT were sampled at...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-13-10
更新日期：2012-01-10 00:00:00
abstract：BACKGROUND:Microarray-based Comparative Genomic Hybridisation (CGH) has been used to assess genetic variability between bacterial strains. Crucial for interpretation of microarray data is the availability of a reference to compare signal intensities to reliably determine presence or divergence each DNA fragment. Howeve...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-10-522
更新日期：2009-11-13 00:00:00
abstract：BACKGROUND:Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecili...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-019-5694-1
更新日期：2019-05-09 00:00:00
abstract：BACKGROUND:Maternal undernutrition leads to an increased risk of metabolic disorders in offspring including obesity and insulin resistance, thought to be due to a programmed thrifty phenotype which is inappropriate for a subsequent richer nutritional environment. In a rat model, both male and female offspring of undern...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-15-49
更新日期：2014-01-21 00:00:00
abstract：BACKGROUND:Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epig...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-018-4814-7
更新日期：2018-06-04 00:00:00
abstract：BACKGROUND:JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the geno...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-018-5075-1
更新日期：2018-09-19 00:00:00
abstract：BACKGROUND:Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received l...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-016-2969-7
更新日期：2016-08-08 00:00:00
abstract：BACKGROUND:Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. RESULTS:Comparative analysis showed that the structure and evolutionary patterns of the I...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-15-743
更新日期：2014-08-30 00:00:00
abstract：BACKGROUND:Natural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and genetically programmed responses to these toxic chemicals, but mechanistic understanding of such is...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-9-266
更新日期：2008-06-03 00:00:00
abstract：BACKGROUND:The sacred lotus (Nelumbo nucifera) is widely cultivated in China for its edible rhizomes and seeds. Traditional plant breeding methods have been used to breed cultivars with increased yields and quality of rhizomes and seeds with limited success. Currently, the available genetic maps and molecular markers i...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/s12864-016-2781-4
更新日期：2016-06-17 00:00:00
abstract：BACKGROUND:Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of endobiotics is also modulated, resulting in potentially harmful effects. We therefore used 1,4-Bis ...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-10-384
更新日期：2009-08-19 00:00:00
abstract：BACKGROUND:The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown th...
journal_title：BMC genomics
pub_type： 杂志文章
doi：10.1186/1471-2164-10-185
更新日期：2009-04-24 00:00:00
