1 / 6

Jessica Dantzer Mooney Lab Center for Computational Biology and Bioinformatics

Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource. Acknowledgements. Support. Jessica Dantzer Mooney Lab Center for Computational Biology and Bioinformatics Indiana University School of Medicine jessica.dantzer@compbio.iupui.edu. CCBB

johnathane
Download Presentation

Jessica Dantzer Mooney Lab Center for Computational Biology and Bioinformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource Acknowledgements Support Jessica Dantzer Mooney Lab Center for Computational Biology and Bioinformatics Indiana University School of Medicine jessica.dantzer@compbio.iupui.edu • 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.

  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. SeqMap Workflow Workflow

  4. SeqMap: an automated tool

  5. SeqMap: genome mapping • 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

  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

More Related