ArticleBMC genomics2014
Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Deciphering the complex molecular architecture of the genetically modified soybean FG72 through paired-end whole genome sequencing.Food chemistry. Molecular sciences · 2025Article
- Genomic and biochemical comparison of allelic triple-mutant lines derived from conventional breeding and multiplex gene editing.The plant genome · 2025Article
- Development and performance evaluation of whole-genome sequencing with paired-end and mate-pair strategies in molecular characterization of GM crops: One GM rice 114-7-2 line as an example.Food chemistry. Molecular sciences · 2022Article
- LIFE-Seq: a universal Large Integrated DNA Fragment Enrichment Sequencing strategy for deciphering the transgene integration of genetically modified organisms.Plant biotechnology journal · 2022Article
- TC-hunter: identification of the insertion site of a transgenic gene within the host genome.BMC genomics · 2022Article
- Article
- Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines.BMC biotechnology · 2020Article
- Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis.Genome research · 2019Article
- Transgenic and physiological mouse models give insights into different aspects of amyotrophic lateral sclerosis.Disease models & mechanisms · 2019Review
- CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula.Plant biotechnology journal · 2018Article
- Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes.Frontiers in molecular neuroscience · 2018Article
- Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification.Nucleic acids research · 2017Article
- Chromosomal mapping of the αMHC-MerCreMer transgene in mice reveals a large genomic deletion.Transgenic research · 2016Article
- Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.Analytical and bioanalytical chemistry · 2016Review
- Efficient generation of transgenic cattle using the DNA transposon and their analysis by next-generation sequencing.Scientific reports · 2016Article
- Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants.BMC biotechnology · 2016Article
- Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.PloS one · 2016Article
- CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing.Genomics data · 2015Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundTransgenesis by random integration of a transgene into the genome of a zygote has become a reliable and powerful method for the creation of new mouse strains that express exogenous genes, including human disease genes, tissue specific reporter genes or genes that allow for tissue specific recombination. Nearly 6,500 transgenic alleles have been created by random integration in embryos over the last 30 years, but for the vast majority of these strains, the transgene insertion sites remain uncharacterized.
resultsTo obtain a complete understanding of how insertion sites might contribute to phenotypic outcomes, to more cost effectively manage transgenic strains, and to fully understand mechanisms of instability in transgene expression, we've developed methodology and a scoring scheme for transgene insertion site discovery using high throughput sequencing data.
conclusionsSimilar to other molecular approaches to transgene insertion site discovery, high-throughput sequencing of standard paired-end libraries is hindered by low signal to noise ratios. This problem is exacerbated when the transgene consists of sequences that are also present in the host genome. We've found that high throughput sequencing data from mate-pair libraries are more informative when compared to data from standard paired end libraries. We also show examples of the genomic regions that harbor transgenes, which have in common a preponderance of repetitive sequences.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.