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Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource

Gene Therapy volume 15, pages 1294–1298 (2008)Cite this article

Abstract

Research in gene therapy involving genome-integrating vectors now often includes analysis of vector integration sites across the genome using methods such as ligation-mediated PCR (LM-PCR) or linear amplification-mediated PCR (LAM-PCR). To help researchers analyze these sites and the functions of nearby genes, we have developed SeqMap (http://seqmap.compbio.iupui.edu/) a secure, web-based comprehensive vector integration site management tool that automatically analyzes and annotates large numbers of vector integration sites derived from LM-PCR experiments in human and model organisms upon a common genome database. We believe the use of this resource will enable better reproducibility and understanding of this important data.

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Acknowledgements

We would like to thank Robert Getty, Susan Jean Johns and Giselle Knudsen for helpful comments. Funding provided by P01HL53586 (PI: Dinauer), S Dirscherl was funded by NIH T32 CA111198, K22LM009135 (PI: Mooney), the Indiana University Vector Production Facility (U42RR11148, PI: Cornetta), R01HG04359 (PI:Li) and INGEN. The Indiana Genomics Initiative (INGEN) is funded in part by a grant from the Lilly.

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Authors and Affiliations

  1. Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA

    B Peters, J Dantzer, J Nowacki, X Li & S D Mooney

  2. Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA

    S Dirscherl & M C Dinauer

  3. Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA

    S Cross, K Cornetta, M C Dinauer & S D Mooney

  4. Division of Biostatistics, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA

    X Li

  5. Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA

    K Cornetta

  6. Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA

    K Cornetta & M C Dinauer

  7. Section of Pediatric Hematology/Oncology, Riley Hospital for Children, Indianapolis, IN, USA

    M C Dinauer

Authors
  1. B Peters
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  2. S Dirscherl
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  3. J Dantzer
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  4. J Nowacki
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  5. S Cross
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  6. X Li
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  7. K Cornetta
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  8. M C Dinauer
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  9. S D Mooney
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Corresponding author

Correspondence to S D Mooney.

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Peters, B., Dirscherl, S., Dantzer, J. et al. Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource. Gene Ther 15, 1294–1298 (2008). https://doi.org/10.1038/gt.2008.99

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