Genomic Analysis Core

点击翻译按钮获取中文摘要

PROJECT SUMMARY – Genomic Analysis Core The Genomic Analysis Core (GAC) of the Abramson Cancer Center (ACC) provides a spectrum of genomic and molecular biological services with a team of highly experienced and trained professionals. These services are essential to ACC members for studying the role of specific genes in normal or abnormal cellular processes found in cancer cells and tumors. Investigators can observe global gene expression patterns in a sample, and genetic variability in an unaffected or tumor genome. The GAC's configuration dates to 2014 when two NCI CCSG supported Shared Resources – the DNA Sequencing Facility and the Genomics Facility – were consolidated under a single umbrella facility. The resulting Shared Resource was and continues to be directed by Dr. Tapan Ganguly, who directed the DNA Sequencing Facility since 2003. He is assisted by Erik Toorens, Technical Director, with five years of leadership and fifteen years of service at the GAC. This team is supported by seven other FTEs with an average of fifteen years' experience. GAC offers sequencing service on three platforms - Ion Torrent PGM & S5, Illumina MiSeq & NextSeq 500 - and Sanger sequencing on ABI capillary sequencers. The capillary sequencers also enable microsatellite-based genotyping, fragment analysis, and cell line authentication. Whole genome and targeted molecular profiling are performed on multiple platforms. The GAC supports quantitative RNA and DNA profiling on Affymetrix GeneChips and high-throughput GeneTitan, Fluidigm BioMark HD, and ABI QS12 Flex real-time PCR instruments. The molecular biological services include cloning, subcloning, site-directed mutagenesis and vector construction. ACC members benefit from consultations and training available throughout their projects. The range of services along with the expertise of the GAC Director facilitates gene discovery, functional characterization and other research questions to elucidate the molecular pathogenesis of human cancers. In addition, molecular profiling of DNA and RNA, together with targeted sequencing of cancer genes, can help ACC members in cancer diagnosis, subclassifications, risk prediction and selection of appropriate therapy. The GAC contributed to multiple high impact publications, including supporting the generation of RNA-Seq and ATAC-Seq data to elucidate tumor- specific characteristics that underlie variability of immune cell infiltration and response to immunotherapy using a mouse pancreatic cancer model (Li et al., Immunity, 2018; Markosyan et al., J Clin Invest, 2019). ACC members accounted for 102 of 376 investigators (27%) using the Shared Resource during the most recent reporting period (07/01/18-06/30/19). In addition to CCSG support, funding for the GAC comes from chargebacks, grants/contracts and Institutional support, including funding for equipment purchases. The excellent scientific and technical management of this facility, along with highly qualified and stable staff, contribute to the reputation of this well-established and effective Shared Resource as an integral part of the infrastructure necessary for rigorous cancer research.