Comprehensive investigation of parameter choice in viral integration site analysis and its effects on the gene annotations produced

Human Gene Therapy

Volumn 23, Issue 11, 2012, Pages 1209-1219

  Huston, Marshall W ^a   Brugman, Martijn H ^a,b   Horsman, Sebastiaan ^a   Stubbs, Andrew ^a   Van Der Spek, Peter ^a   Wagemaker, Gerard ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CD34 ANTIBODY; RETROVIRUS VECTOR;

ADENOSINE DEAMINASE DEFICIENCY; ANALYTICAL PARAMETERS; ARTICLE; COMPARATIVE STUDY; COMPUTER INTERFACE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENE ACTIVITY; GENE EXPRESSION; GENE SEQUENCE; METHOD FOR ANALYZING VIRUS INTEGRATION COLLECTION; POSITION EFFECT; SEQUENCE ANALYSIS; VIRAL GENE THERAPY; VIRUS DNA CELL DNA INTERACTION; VIRUS GENOME; WEB BROWSER; X LINKED SEVERE COMBINED IMMUNODEFICIENCY;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENETIC VECTORS; GENOME; HEMATOPOIETIC STEM CELLS; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MUTAGENESIS, INSERTIONAL; RETROVIRIDAE; SEVERE COMBINED IMMUNODEFICIENCY; VIRUS INTEGRATION;

EID: 84869049596     PISSN: 10430342     EISSN: 15577422     Source Type: Journal    
DOI: 10.1089/hum.2011.037     Document Type: Article

References (32)

1. Aiuti, A., Slavin, S., Aker, M., et al. (2002). Correction of ADASCID by stem cell gene therapy combined with nonmyeloablative conditioning. Science 296, 2410-2413.
2. Aiuti, A., Cassani, B., Andolfi, G., et al. (2007). Multilineage hematopoietic reconstitution without clonal selection in ADASCID patients treated with stem cell gene therapy. The Journal of Clinical Investigation 117, 2233-2240.
3. Altschul, S.F., Gish, W., Miller, W., et al. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.
4. Appelt, J.U., Giordano, F.A., Ecker, M., et al. (2009). QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis. Gene Therapy 16, 885-893.
5. Bartholomew, C., and Ihle, J.N. (1991). Retroviral insertions 90 kilobases proximal to the Evi-1 myeloid transforming gene activate transcription from the normal promoter. Molecular and Cellular Biology 11, 1820-1828.
6. Biasco, L., Ambrosi, A., Pellin, D., et al. (2011). Integration profile of retroviral vector in gene therapy treated patients is cell-specific according to gene expression and chromatin conformation of target cell. EMBO Molecular Medicine 3, 89-101.
7. Deichmann, A., Hacein-Bey-Abina, S., Schmidt, M., et al. (2007). Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy. The Journal of Clinical Investigation 117, 2225-2232.
8. Deichmann, A., Brugman, M.H., Bartholomae, C., et al. (2011). Insertion sites in engrafted cells cluster within a limited repertoire of genomic areas after gammaretroviral vector gene therapy. Molecular Therapy 19, 2031-2039.
9. Erkeland, S.J., Verhaak, R.G., Valk, P.J., et al. (2006). Significance of murine retroviral mutagenesis for identification of disease genes in human acute myeloid leukemia. Cancer Research 66, 622-626.
10. Flicek, P., Amode, M.R., Barrell, D., et al. (2011). Ensembl 2011. Nucleic Acids Research 39, D800-806.
11. Gaspar, H.B., Parsley, K.L., Howe, S., et al. (2004). Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector. Lancet 364, 2181-2187.
12. Hacein-Bey-Abina, S., Le Deist, F., Carlier, F., et al. (2002). Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy. The New England Journal of Medicine 346, 1185-1193.
13. Hawkins, T.B., Dantzer, J., Peters, B., et al. (2011). Identifying viral integration sites using SeqMap 2.0. Bioinformatics 27, 720-722.
14. Horsman, S., Huston, M., Stubbs A. (2011). MAVRIC: methods for analyzing viral integration clusters. http://mavric .erasmusmc.nl/
15. Joosten, M., Vankan-Berkhoudt, Y., Tas, M., et al. (2002). Largescale identification of novel potential disease loci in mouse leukemia applying an improved strategy for cloning common virus integration sites. Oncogene 21, 7247-7255.
16. Kustikova, O., Fehse, B., Modlich, U., et al. (2005). Clonal dominance of hematopoietic stem cells triggered by retroviral gene marking. Science 308, 1171-1174.
17. Kustikova, O.S., Modlich, U., and Fehse, B. (2009). Retroviral insertion site analysis in dominant haematopoietic clones. Methods in Molecular Biology 506, 373-390.
18. Levy, S., Sutton, G., Ng, P.C., et al. (2007). The diploid genome sequence of an individual human. PLoS Biology 5, e254.
19. Lewinski, M.K., Yamashita, M., Emerman, M., et al. (2006). Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathogens 2, e60.
20. Li, W., and Gozick, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659.
21. Mikkers, H., Allen, J., Knipscheer, P., et al. (2002).High-throughput retroviral tagging to identify components of specific signaling pathways in cancer. Nature Genetics 32, 153-159.
22. Mitchell, R.S., Beitzel, B.F., Schroder, A.R., et al. (2004). Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biology 2, E234.
23. Modlich, U., Kustikova, O.S., Schmidt, M., et al. (2005). Leukemias following retroviral transfer of multidrug resistance 1 (MDR1) are driven by combinatorial insertional mutagenesis. Blood 105, 4235-4246.
24. Modlich, U., Navarro, S., Zychlinski, D., et al. (2009) Insertional transformation of hematopoietic cells by self-inactivating lentiviral and gammaretroviral vectors. Molecular Therapy 17, 1919-1928.
25. Montini, E., Cesana, D., Schmidt, M., et al. (2006). Hematopoietic stem cell gene transfer in a tumor-prone mouse model uncovers low genotoxicity of lentiviral vector integration. Nature Biotechnology 24, 687-696.
26. Montini, E., Cesana, D., Schmidt, M., et al. (2009). The genotoxic potential of retroviral vectors is strongly modulated by vector design and integration site selection in a mouse model of HSC gene therapy. The Journal of Clinical Investigation 119, 964-975.
27. Pruitt, K.D., Tatusova, T., and Maglott, D.R. (2007). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35, D61-65.
28. Schro der, A.R.W., Shinn, P., Chen, H., et al. (2002). HIV-1 integration in the Human Genome Favors Active Genes and Local Hotspots. Cell 110, 521-529.
29. Schwarzwaelder, K., Howe, S.J., Schmidt, M., et al. (2007). Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo. The Journal of Clinical Investigation 117, 2241-2249.
30. Wu, X., Li, Y., Crise, B., and Burgess, S.M. (2003). Transcription start regions in the human genome are favored targets for MLV integration. Science 300, 1749-1751.
31. Zeeberg, B.R., Riss, J., Kane, D.W., et al. (2004). Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics 5, 80.
32. Zychlinski, D., Schambach, A., Modlich, U., et al. (2008). Physiological promoters reduce the genotoxic risk of integrating gene vectors. Molecular Therapy 16, 718-725.