Shared Resource: Genomics Facility

Research Inst Of Fox Chase Can Ctr, Philadelphia PA

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Abstract

CELLULAR/MOLECULAR ANALYSES SHARED RESOURCE: GENOMICS FACILITY (GF) PROJECT SUMMARY/ABSTRACT The Genomics Facility (GF) provides cost-effective, high-quality genomic and epigenetic services that facilitate the science of Cancer Center members. The GF is under the direction of Joseph Testa, PhD (CB), and supported by 3 FTE Managers and 1.35 FTE technical staff. The GF offers three major research service Units: Research Cytogenetics and Chromosome Microarray Analysis (CMA), Expression Microarray and NextGen Sequencing; and Genotyping & Real-Time PCR. The GF is located in contiguous laboratory space on the 3rd floor of the Robert C. Young, MD Pavilion, a location that is centrally located and easily accessible to all Cancer Center members. The GF addresses the genomic and gene expression needs of Cancer Center members, many of whom conduct research aimed at understanding the genetic and epigenetic underpinnings of tumor formation and progression. The GF assists investigators to unravel biomarkers or molecular signatures of cancer that may improve patient care by affording advances in the early detection, diagnosis and treatment of cancer, important FCCC objectives. Additionally, the GF holds several scientific and technical seminars annually to present applications of new genomic platforms for cancer research. Overall, the services provided by the GF are a valuable resource, as they help to support research efforts in all five Research Programs and sustain the translational research objectives of the Center. 41 Cancer Center members used the GF in calendar year 2014, of which 88% had peer-review-funded grants. 63 Cancer Center members from all 5 Research Programs used the GF in the period 2011-2014. The experience of the Facility Director, Testa, is key in implementing state-of-the-art technology and new approaches. Testa's leadership coupled with investment of $42,000 led to upgrading the Illumina HiSeq2500. The HiSeq 2500 can perform a full line of high throughput sequencing applications and is capable of generating 600 GB of data in 11 days in the high output mode and 120 GB in 1 day in the rapid mode. The Center also provided funds of $231,000 for a nanoString's nCounter Analysis System that enables the profiling of hundreds of mRNAs, microRNAs, or CNVs simultaneously with high sensitivity and precision. The primary benefits of the platform are the ability to complete studies faster and with very high precision. A major value added of the GF is that it is the most cost effective way to provide users with advanced technologies that are too costly to purchase and support by any individual lab. The GF staff provides stability by ensuring users access to properly functioning instruments. The GF is advised by a dedicated Facility Advisory Committee (FAC) that meets at least annually. Recommendations from the FAC are directed to a governing Facility Parent Oversight Committee (FPOC) that serves to ensure that the GF continues to have the necessary resources to provide the highest quality genomic and epigenetic services for Cancer Center members. Demand for services is expected to increase in the next cycle of the CCSG due to plans to recruit in all 5 Research Programs, and new demand from TU.