Genomics

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ABSTRACT – Sequencing and Genomics (GEN) Shared Resource The Sequencing and Genomics Shared Resource (GEN SR) is a ‘super SR’ that provides an integrated platform of technology, expertise, education, and infrastructure creating an accessible environment for LCCC researchers to design and undertake cutting edge genomics projects. This SR is led by a team of highly experienced genomic biologists with proven track records in cancer-related research. The SR specializes in five major technologies: Agilent Microarrays, Affymetrix Microarrays, Illumina bead array genotyping, NextGen sequencing (Illumina, PacBio, and Ion Platforms) and RNAi screening for functional validation. These areas are complemented by major LCCC investments in computational infrastructure and analysis. The SR provides state-of-the-art equipment and specialized expertise to guide users through any and all stages of a project: consultation, sample QC, data generation, and analysis. These services are being used by LCCC researchers to understand fundamental cellular processes that contribute to cancer. For example, these facilities have contributed extensively to the data generated at UNC as part of The Cancer Genome Atlas project. Additionally, several groups are using these SRs to translate cancer genomic information into actionable clinical data as part of the NCGENES and UNCseq projects. In addition to an increase in these translational projects, we expect that the next five years there will be increased demand for integrative genomics projects that generate data from a variety of sources and SRs and then, working with the Bioinformatics Shared Resource teams, produce comprehensive analyses of tumor samples. From the end of June 2013 to July 2014, the GEN SR was used by 96 LCCC members (85% of total use). Since 2009 use of this combined facility has nearly tripled (measured in terms of grant and recharge dolla rs). Highlights for the GEN SR during the last funding period include extensive expansion of our NextGen sequencing services and automation of all array platforms, as well as relocation to a new shared facility space custom renovated to support the specific infrastructure required to run these systems 24/7. As a result, in fiscal year 2013-2014 alone this SR made 13,303 genomic libraries, sequenced over 100 Trillion bp, genotyped 1,945,409,504 SNPs, and ran 13,517 microarray experiments. This work has contributed to over a hundred publications, including seven in Nature as part of The Cancer Genome Atlas project. For 2015, the LCCC requests $254,659 to maintain personnel to support genomics efforts and offset service contract costs. CCSG funds are projected to be 4% of operating costs.