1. 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 research 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. AcknowledgementsSupport

2. 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

3. Workflow SeqMap Workflow

4. SeqMap: an automated tool

5. 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

6. Future Collect publicly available gene therapy data and incorporate into site –Working with Indiana University Vector Production Facility to collect data Future additions to the SeqMap tool also include –analysis of functional annotations