Core-005

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ABSTRACT The University of Chicago Medicine Comprehensive Cancer Center (UCCCC) Genomics Core Facility (GCF) is tasked with providing state-of-the-art genomics data generation services to University of Chicago faculty in a fee-for-service model. UCCCC members’ fees are subsidized by the Cancer Center Support Grant (CCSG) via a co-pay mechanism. At present, the GCF main services are next-generation sequencing, DNA microarray analysis, and Sanger sequencing. The GCF also provides data storage services to its clients and partners with the Bioinformatics Core Facility (BiCF) for genomic data analysis. The GCF is organized into two Subcores, Next-Generation Sequencing and Microarrays Subcore, and DNA Sequencing and Genotyping Subcore, and has been located on the first floor of the Knapp Center for Biomedical Discovery (KCBD) since 2009. The GCF is directed scientifically by Yoav Gilad, PhD, Professor of Human Genetics, and operationally by Pieter Faber, PhD, with the assistance of William Buikema, PhD, as Technical Director of the DNA Sequencing and Genotyping Subcore. In addition to the leadership, the GCF employs nine technologists (six in the NextGeneration Sequencing and Microarrays Subcore, and three in the DNA Sequencing and Genotyping Subcore). Core developments in the current funding period include increased emphasis on next-generation sequencing (NGS) services to meet demand and advancements in the field. The main operating instruments of the Facility include Applied Biosystems 3730xl DNA analyzers (DNA Sequencing and Genotyping Subcore), an Illumina HiScan, and an Affymetrix GeneScan3000 microarray scan system, as well as three Illumina nextgeneration sequencing instruments (HiSEQ4000, HiSEQ2500, and a NextSeq500; Next-Generation Sequencing and Microarrays Subcore). The GCF effectively serves users’ needs, and the services provided using these instruments occupy 80-90% of the available instrument and/or personnel time, indicating that staffing and instrumentation are operating and maintained at an appropriate level. UCCCC members receive priority, and projects are prioritized based on sample reception date and project urgency. To direct operations, Drs. Gilad and Faber meet on a biweekly basis, discussing any operational issues, as well as short-term and long-term strategies. Additionally, Drs. Gilad and Faber meet regularly with the GCF Faculty Oversight Committee (FOC) to receive constructive feedback from expert users in the genomics field. To best serve users’ needs and gauge user satisfaction, the University of Chicago Office of Shared Research Facilities under the leadership of George Langan, DVM, conducts annual on-campus user surveys. The most recent survey from August 2016 showed a high approval rating (approximately 80%), with 99% of responders predicting continued use of the Facility in the future. New services will be added as needed (e.g., the Facility intends to add single cell RNA-SEQ to its repertoire (DROP-SEQ protocol) in 2017).