Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.
%0 Journal Article
%1 Appelt.2009
%A Appelt, J-U
%A Giordano, F. A.
%A Ecker, M.
%A Roeder, I.
%A Grund, N.
%A Hotz-Wagenblatt, A.
%A Opelz, G.
%A Zeller, W. J.
%A Allgayer, H.
%A Fruehauf, S.
%A Laufs, S.
%D 2009
%J Gene therapy
%K Access_to_Information Animals Automatic_Data_Processing/methods Base_Sequence/genetics Binding_Sites Chromosome_Fragile_Sites Chromosome_Mapping/methods Computational_Biology/methods CpG_Islands Databases,_Genetic Genetic_Therapy/methods/standards Genetic_Vectors/adverse_effects/therapeutic_use Genome,_Human/genetics Humans Mice Molecular_Sequence_Data Mutagenesis,_Insertional/genetics Polymerase_Chain_Reaction/methods Repetitive_Sequences,_Nucleic_Acid Retroviridae/genetics Safety Sequence_Analysis,_DNA/methods Software
%N 7
%P 885–893
%T QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis
%V 16
%X Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.
@article{Appelt.2009,
abstract = {Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.},
added-at = {2014-10-15T15:03:37.000+0200},
author = {Appelt, J-U and Giordano, F. A. and Ecker, M. and Roeder, I. and Grund, N. and Hotz-Wagenblatt, A. and Opelz, G. and Zeller, W. J. and Allgayer, H. and Fruehauf, S. and Laufs, S.},
biburl = {https://www.bibsonomy.org/bibtex/28729534a30a1a3e8eed3d7e42f1e7e86/drtester},
interhash = {cae7caf0a4595fe3901a3183c6c3b208},
intrahash = {8729534a30a1a3e8eed3d7e42f1e7e86},
journal = {Gene therapy},
keywords = {Access_to_Information Animals Automatic_Data_Processing/methods Base_Sequence/genetics Binding_Sites Chromosome_Fragile_Sites Chromosome_Mapping/methods Computational_Biology/methods CpG_Islands Databases,_Genetic Genetic_Therapy/methods/standards Genetic_Vectors/adverse_effects/therapeutic_use Genome,_Human/genetics Humans Mice Molecular_Sequence_Data Mutagenesis,_Insertional/genetics Polymerase_Chain_Reaction/methods Repetitive_Sequences,_Nucleic_Acid Retroviridae/genetics Safety Sequence_Analysis,_DNA/methods Software},
number = 7,
pages = {885–893},
timestamp = {2014-10-15T15:03:37.000+0200},
title = {QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis},
volume = 16,
year = 2009
}