Genomics

Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA

Investigators

Linked publications & trials

Abstract

5.5 Abstract - GENOMICS (Group B Core) The Genomics Shared Resource (Core Group B) operates as a full service nucleic acid to data facility, guiding investigators to the most appropriate technology for their experimental analysis, including next- generation sequencing (NGS), microarrays, NanoString, or Q-PCR. The Core has two major areas of focus. These are DNA Analysis, providing high throughput sequencing and data analysis, and Microarray/Q-PCR effort, providing Illumina-based microarray analysis, as well as full-service real-time PCR analysis. During the last funding period the DNA Analysis Core has added significant NGS capacity and personnel, and is now primarily focused on providing NGS services for Cancer Center investigators. Additionally, the previously separate microarray/QPCR and DNA analysis facilities have been co-located and operationally combined to augment NGS capacity, and streamline service. For NGS projects, the Core provides a complete sample-to- analyzed data service. Such data outputs include differential expression and differential splicing analysis for RNA-seq projects, and annotated variant calls for DNA-seq projects. Enhancements in NGS technology include the addition of an Ion Torrent Personal Genome Machine (PGM), an Ion Proton sequencer, and an Ion Chef Sample preparation system. The Ion Proton sequencer currently has the capacity to sequence 20 human exomes or 30 transcriptomes per week. The PGM has been popular for sequencing targeted gene panels (e.g., Cancer AmpliSeq panels) and small genomes. In addition, a new DNA Analysis Core director with NGS and Bioinformatics experience was recruited in May of 2013. The Facility has received external validation as an Ion AmpliSeq Exome Certified Service Provider by Life Technologies. The Core works closely with the Bioinformatics Shared Resource to assist users with additional downstream analysis, or custom applications of NGS technology. The Microarray Q-PCR service continues to see significant demand, performing 800 Illumina arrays quantitating gene expression and 8000 full service Q-PCR reactions in the past year. The Facility uses the Illumina bead-based microarray system and provides full service array analysis, taking in RNA samples from investigators, performing QC, and then performing array analysis through to initial data analysis using the Illumina GenomeStudio software. Global gene expression analysis is performed using the Illumina BeadStation 500X microarray system, utilizing the cost-effective Illumina HT 48K human gene arrays, or for mouse gene expression analysis, either 8x1 24K or 6x2 48K arrays. For QPCR services, the Facility has a dedicated Roche LC480 (96 and 384 well blocks) and a Stratagene MP3000 96 well real-time PCR instruments. The Core also assists users of the NanoString nCounter for amplification-free RNA Analysis, as well as support for a variety of shared-use analytical instruments. Overall, the Genomics Shared Resource continues to provide broad support to the Cancer Center, with its services utilized in the past funding period by 45 Cancer Center laboratories representing all 3 programs, and has contributed to over 88 cancer-related publications.