jessica dantzer mooney lab center for computational biology and bioinformatics indiana university...
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Jessica Dantzer
Mooney Lab
Center for Computational Biology and Bioinformatics
Indiana University School of Medicine
jessica.dantzer@compbio.iupui.edu
Automated analysis of viral integration sites in gene therapy Automated analysis of viral integration sites in gene therapy research using the SeqMap web resourceresearch using the SeqMap web resource
• CCBB– Sean D. Mooney– Xiaoman Li– Brandon Peters
• Herman B Wells Center for Pediatric Research– Sara Dirscherl– Mary C. Dinauer
• Department of Medical & Molecular Genetics– Scott Cross– Kenneth Cornetta
• Others– Robert Getty– Susan Jean Johns– Giselle Knudsen
Funding provided by: • P01HL53586 (PI: Dinauer) • K22LM009135 (PI: Mooney)• The Indiana University Vector Production Facility• INGEN.
The Indiana University Vector Production Facility is a NIH designated National Gene Vector Laboratory (U42RR11148, PI: Cornetta).
The Indiana Genomics Initiative (INGEN) is funded in part by a grant from the Lilly Endowment.
Acknowledgements Support
What is gene therapy?• Cells affected by diseases caused by “broken” genes can be aided
by the addition of “working” genes
• Working genes are carried by a vector, in most cases an altered virus, into an individual’s cells
• Working genes which are incorporated into the cell then produce their protein products, correcting the cell’s malfunction
• So cells will continue to create copies of inserted DNA, new gene needs to integrate into cell’s DNA– Altered retroviruses (disease-causing genetic material removed)
integrate their genetic material into the host organism’s
• Insertional mutagenesis-- Insertion disrupts DNA sequence and causes changes in nearby gene expression
• Genes within 300kbp of the integration site are found using BLAT (BLAST-like alignment tool) on local copies of UCSC and Ensembl
• Functional analysis is provided by noting genes found in the Retroviral Tagged Cancer Gene Database (RTCGD) and associated Gene Ontology (GO) terms
SeqMap: genome mapping
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