Genomics

University Of California At Davis, Davis CA

Investigators

Linked publications, trials & patents

Abstract

PROJECT SUMMARY/ABSTRACT The Genomics Shared Resource (GSR) provides comprehensive services and expertise in the area of genomics and data analysis and bioinformatics. The GSR provides Cancer Center researchers with direct access to the most contemporary genomic applications and state-of-the-art instrumentation for next-generation sequencing (NGS), microarray analyses, and NanoString nCounter analyses. This includes Illumina NGS systems (MiSeq, HiSeq 2500, 3000, 4000), multi-platform microarray processing equipment for Affymetrix, Agilent, and Illumina microarrays, and the required computational hardware and software systems. Together, these enable investigators to accomplish virtually every type of application for transcriptomics, genome sequencing, epigenomics, and metagenomics, including whole transcriptome analysis, genome-wide profiling of single nucleotide variants, copy number analysis, mapping of long-range interactions of DNA regions, and molecular characterization of infectious agents. These are generally provided as completely comprehensive, sample-to-results services in that investigators need only provide RNA or DNA samples, and the GSR will perform all downstream technical processing, as well as data analysis. Ancillary services for DNA/RNA isolation, quality assessment, and sample acquisition are also provided. To complement these services and to help achieve productive outcomes from genomics experiments, the GSR provides extensive data analysis and integrative bioinformatics support, and routinely assists in the preparation of the appropriate sections of manuscripts and grant proposals. Additionally, education is an important component of the GSR and is provided through training, workshops, and seminars. Unique aspects of the GSR include a strong emphasis on facilitating translational science and the custom development of protocols and reagents to address the specific goals of investigators' experiments. For translational applications, the GSR has developed and optimized protocols enabling the analysis of samples obtained from clinical specimens, such as whole blood, serum/plasma, and FFPE specimens. Investigator-driven research often requires protocols and tools to be adapted or newly developed. These include modified sequencing library preparations and target enrichment panels for mutation screening of tumors and oncogenic viruses. Moreover, the GSR strives to introduce new technologies, such as single-cell sequencing and to serve as a pipeline for clinical applications of genomics. Taken together, the GSR provides a complete integrative and functional molecular profiling solution to the Cancer Center.