Show simple item record

dc.contributor.authorHolman, Alexander G
dc.contributor.authorMefford, Megan E.
dc.contributor.authorO'Connor, Niall
dc.contributor.authorGabuzda, Dana Helga
dc.date.accessioned2011-03-25T16:18:21Z
dc.date.issued2010
dc.identifier.citationHolman, Alexander G., Megan E. Mefford, Niall O'Connor, and Dana Gabuzda. 2010. HIVBrainSeqDB: A database of annotated HIV envelope sequences from brain and other anatomical sites. AIDS Research and Therapy 7: 43.en_US
dc.identifier.issn1742-6405en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4774090
dc.description.abstractBackground: The population of HIV replicating within a host consists of independently evolving and interacting sub-populations that can be genetically distinct within anatomical compartments. HIV replicating within the brain causes neurocognitive disorders in up to 20-30% of infected individuals and is a viral sanctuary site for the development of drug resistance. The primary determinant of HIV neurotropism is macrophage tropism, which is primarily determined by the viral envelope (env) gene. However, studies of genetic aspects of HIV replicating in the brain are hindered because existing repositories of HIV sequences are not focused on neurotropic virus nor annotated with neurocognitive and neuropathological status. To address this need, we constructed the HIV Brain Sequence Database. Results: The HIV Brain Sequence Database is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Patient coding is correlated across studies, allowing sequences from the same patient to be grouped to increase statistical power. Using Cytoscape, we visualized relationships between studies, patients and sequences, illustrating interconnections between studies and the varying depth of sequencing, patient number, and tissue representation across studies. Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. Conclusions: This online resource, which is publicly available at http://www.HIVBrainSeqDB.org, will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection.en_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofdoi:10.1186/1742-6405-7-43en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018377/pdf/en_US
dash.licenseLAA
dc.titleHIVBrainSeqDB: A Database of Annotated HIV Envelope Sequences from Brain and Other Anatomical Sitesen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalAIDS Research and Therapyen_US
dash.depositing.authorGabuzda, Dana Helga
dc.date.available2011-03-25T16:18:21Z
dash.affiliation.otherHMS^Neurology-Brigham and Women's Hospitalen_US
dc.identifier.doi10.1186/1742-6405-7-43*
dash.contributor.affiliatedGabuzda, Dana


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record