Integration Site Analysis

Fig.1 Schematic outline of LAM PCR.

Viral vectors have been successfully used in clinical gene therapy to obtain stable expression of the transgene and therefore long-term correction of the disease. However, the integration of viral vectors at certain genomic locations can not only alter gene expression but also can lead to various side-effects, such as insertional activation of proto-oncogenes, uncontrolled clonal proliferation or the generation of new gene isoforms. Therefore, the analysis of viral vector integration site (IS) in target cells is of vital importance to illuminate and ensure the safety of the therapeutic vector system. Creative Biogene, as one of the leading biotechnology company in the world, has extensive expertise and experience which can offer three different technologies to help you analyze the viral vector insertion/integration sites. Characteristics of the three different technologies is shown below. You can choose the analysis method that works best for you based on your needs.

• LAM PCR: a sensitive method, relies on the use of restriction enzymes, introducing a bias into capacity of IS, only semi-quantitative measurement of individual integration sites/clonal contributions.
• EPTS/LM-PCR: comparable sensitivity like LAM-PCR, but with less bias and much more accurate quantitative measurement of each clonal contribution.
• Hybridization-based enrichment sequencing (HES): lower sensitivity than the above two technologies, but higher accurate quantitative. Using this method both integration sites and vector copy number could be studied.

Applications:

• Analysis of the viral vector integration sites in host genomes
• Localization of genetic elements and characterization of unknown flanking DNA
• Assessing vector biosafety and efficacy
• Elucidating biological and clinical issues

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