Translational Genomics Core

ABSTRACT The Translational Genomics Core (TGC) of the Louisiana Cancer Research Consortium (LCRC) was initially created as a standard sequencing facility to support the basic research infrastructure of the School of Medicine. With the support of Phases I and II of COBRE “Mentoring Translational Research in Louisiana”, the LSU School of Medicine and the Louisiana Cancer Research Center (LCRC), the TGC has developed into a state-of-the-art institutional facility capable of implementing a variety of next generation sequencing (NGS) protocols including whole transcriptome, RNASeq, whole exome sequencing, and array-based methylation and SNP analysis, single-cell sequencing and chromatin-immunoprecipitation sequencing (ChIP-seq). The TGC has served multiple projects through the establishment of service contracts and collaborations at the institutional, local and international level. The TGC is now ideally positioned to support the Phase 2 COBRE “Center for Translational Viral Oncology” (CTVO) application. As in the first phase of the CTVO, the Junior Principal Investigators (JPIs) of the proposed projects will have a discounted pricing structure, comprehensive training, instrumentation access, troubleshooting protocols, and data analysis assistance that is linked to multi-institutional informatics pipelines, including the CTVO BBC. The TGC has been instrumental in the acquisition of two P20-SPORE grants: 1) P20CA202922 (PIs Miele and Meade), and a collaboration with Moffitt Cancer Center in Tampa, FL, in which the TGC Director is a research project PI; 2) 5P20CA233374 (PIs Ochoa, Miele). These studies aim to determine correlations between gene markers and obesity/ethnicity in triple negative breast cancer African American and Caucasian patients in Louisiana. The TGC is constantly evolving and updating instrumentation and protocols to ensure that JPIs in Phase 2 CVTO will have cutting-edge capacity to generate high quality data. Latest acquisitions are 10X genomics single-cell and tissue localized sequencing. Dr. Zabaleta maintains a constant collaboration with Dr. Chindo Hicks, Director of the Bioinformatics and Genomics Program in the Department of Genetics, School of Medicine, LSUHSC-New Orleans and CTVO BBC Co-director as well as pipelines to Tulane University Cancer and Viral Bioinformatics through Dr. Erik Flemington. Drs Zabaleta and Hicks coordinate the sequencing (Dr. Zabaleta) and bioinformatics (Dr. Hicks) to provide the best information to the PIs requesting next generation sequencing data from their nucleic acids samples. These research capacity developments strengthen the propensity for Phase 2 CTVO research project and pilot study success and likelihood for NIH funding.