Analyzing the Number of Common Integration Sites of Viral Vectors – New Methods and Computer Programs


Vectors based on γ-retroviruses or lentiviruses have been shown to stably express therapeutical transgenes and effectively cure different hematological diseases.

Molecular follow up of the insertional repertoire of gene corrected cells in patients and preclinical animal models revealed different integration preferences in the host genome including clusters of integrations in small genomic areas (CIS; common integrations sites).

In the majority, these CIS were found in or near genes, with the potential to influence the clonal fate of the affected cell. To determine whether the observed degree of clustering is statistically compatible with an assumed standard model of spatial distribution of integrants, we have developed various methods and computer programs for γ-retroviral and lentiviral integration site distribution.

In particular, we have devised and implemented mathematical and statistical approaches for comparing two experimental samples with different numbers of integration sites with respect to the propensity to form CIS as well as for the analysis of coincidences of integration sites obtained from different blood compartments.

The programs and statistical tools described here are available as workspaces in R code and allow the fast detection of excessive clustering of integration sites from any retrovirally transduced sample and thus contribute to the assessment of potential treatment-related risks in preclinical and clinical retroviral gene therapy studies.

Read the full publication here.

Related Publications

Discover more publications from the GeneWerk team

Systematic comparative study of computational methods for…

Abstract High-throughput sequencing technologies have exposed the possibilities for the in-depth evaluation of T-cell...

Real-Time Definition of Non-Randomness in the Distribution…

Abstract Features such as mutations or structural characteristics can be non-randomly or non-uniformly distributed...

Preclinical evaluation of efficacy and safety of…

Abstract A previously published clinical trial demonstrated the benefit of autologous CD34(+) cells transduced...

Polyclonal long-term repopulating stem cell clones in…

Abstract Hematopoietic bone marrow stem cells generate differentiated blood cells and, when transplanted, may...

Want to get in touch?

Click the button below if you want to find out more about the services
we offer or discuss your next project.

Contact us
I agree to the Privacy Policy and Terms of Service.