Core B - Virus RNA-seq and Bioinformatics core Summary Core B will serve as a hub that brings together clinical resources, informatics expertise, and infrastructure to facilitate the needs of P01 investigators. The unique relationship with Dr. Parsons (LSUHSC ? New Orleans) who leads the NIH-supported LSUHSC/LCRC HIV Clinical and Biospecimen Repository (UG1-CA189854; R01CA142362; NCI AIDS Malignancies Consortium/AIDS Cancer Specimen Resource) housed at the LCRC (Louisiana Cancer Research Consortium) will facilitate the acquisition of valuable Kaposi's sarcoma (KS) and EBV lymphoma tumor specimens from HIV-infected patients. The existing next generation sequence analysis core at Tulane has expertise in a wide array of computational and analysis approaches for processing high information content biological data including a broad range of virus specific methods. The core also has close relationships with local statistical modeling experts, pathway interaction modeling experts, and computer scientists at Tulane (Dept of Math and the Dept of Biostatistics), LSU, and the HBCU, Xavier University of Louisiana (the latter example being a more formal arrangement through a subcontract with Dr. Kun Zhang). Through these relationships, the core will also serve as a conduit to bring together P01 investigators with specific needs, to the appropriate local collaborators. Training and education of P01 PIs, students, postdocs, and technicians are key components of the core operating philosophy. This approach will help investigators achieve an in-depth understanding of their data while at the same time allowing the core to maintain its current low overhead. The core has already merged the hardware capabilities at Tulane with the University of Florida High Performance Computer Center, creating adequate computational resources to satisfy even substantial growth in the five-year project period.
Core B integrates a number of existing assets from Tulane, LSU, Xavier, and the University of Florida, including hardware, infrastructure, scientific expertise and clinical assets, to help foster a synergistic and cross fertilizing environment to help facilitate clinically relevant investigations into lncRNAs, herpesviruses and HIV- associated cancers.
|Sethuraman, Sunantha; Gay, Lauren Appleby; Jain, Vaibhav et al. (2017) microRNA dependent and independent deregulation of long non-coding RNAs by an oncogenic herpesvirus. PLoS Pathog 13:e1006508|
|Zhang, Wensheng; Edwards, Andrea; Flemington, Erik K et al. (2017) Racial disparities in patient survival and tumor mutation burden, and the association between tumor mutation burden and cancer incidence rate. Sci Rep 7:13639|