Genomic Sciences Shared Resource

Vanderbilt University Medical Center, Nashville TN

Investigators

Linked publications, trials & patents

Abstract

BASIC RESEARCH GROUP CORE 006 ? GENOMIC SCIENCES SHARED RESOURCES PROJECT SUMMARY/ABSTRACT The Genomic Sciences Shared Resource (GSSR) provides advanced genomics technologies required to support the full range of cancer research conducted by Vanderbilt-Ingram Cancer Center (VICC) members. This facility provides investigators with state-of-the-art services utilizing a myriad of genotyping and sequencing technology platforms. A unique feature of the facility is the availability and customizability of numerous major genomics technology platforms, which offer exceptional flexibility in analytical approaches. The GSSR service lines include genotyping, high-throughput genotyping, Sanger sequencing and ?next-generation? sequencing, including whole genome, whole exome, targeted re-sequencing, RNA-seq, ChIP-seq and miR-seq. The GSSR also works with investigators to aid in the development of new sequencing strategies such as PRO-seq (precision global nuclear run-on-sequencing) and ChIP-Exo (chromatin immunoprecipitation + exonuclease footprinting-sequencing). As these technologies and standards evolve, the GSSR continues to update capabilities to stay at the forefront of these fields. The resource maintains a bevy of state-of-the-art instruments, including two HiSeq 2500 sequencers, two MiSeq sequencers and links to the advanced computing cluster. Typically, one of the HiSeq instruments is assigned to conventional run mode to accomplish requests such as large exome projects, while the second instrument is used in rapid run mode to facilitate very rapid turnover of smaller projects, most commonly RNA-Seq analysis. The GSSR provides a high level of training and consultation for users of all levels, including providing ?studios? to review cancer-related projects from investigators seeking to use technologies in this resource. Thus, each project receives custom review and input from a highly experienced staff. Storage of data and access to data is paramount in this area, and the GSSR has fully integrated into the institution?s data center and supercomputing cluster to enable rapid and efficient transfer and analysis of data. Data generation is only the first step to a successful experiment and investigators have varying levels of sophistication in the area of data analysis. The GSSR provides essentially raw data (following QC processes to ensure quality) to sophisticated user groups, but also provides data sets with a significant amount of standard analysis to many groups. Access for users to workstations, a large panel of commercial analytical tools and orientation to the uses of these tools is also provided. Most importantly, the GSSR shares a bioinformatician and data manager with the Quantitative Sciences Shared Resource (QSSR); staff are housed in the GSSR to provide investigators with personalized guidance for data analysis and to interface with the advanced analytical services provided by the QSSR when customized analysis is needed.