Genome Analysis Shared Resource

Mayo Clinic Rochester, Rochester MN

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Abstract

GENOME ANALYSIS SHARED RESOURCE: ABSTRACT The Genome Analysis Shared Resource (GENSR) provides Mayo Clinic Comprehensive Cancer Center (MCCCC) researchers efficient, high-quality, cost-effective access to state-of-the-art genomics technologies for studying gene structure and function. Since 2003, the GENSR components at Mayo Clinic in Rochester (MCR) and Mayo Clinic in Florida (MCF) have been working in a coordinated fashion to provide technical expertise, instrumentation, and comprehensive support for nucleic acid sequencing, gene expression profiling, and genotyping to achieve three Specific Aims: Aim 1: Provide MCCCC members with access to personalized and cost-effective technology and expertise that enables comprehensive analysis of genome structure and function. Aim 2: Ensure the quality and integrity of all GENSR workflows through continuous training and implementation of a rigorous quality management program. Aim 3: Continually upgrade GENSR service lines and instruments to remain a state-of-the-art resource for the MCCCC community. The services provided by the GENSR include deep-sequencing studies of RNA and DNA on Illumina NovaSeq, NextSeq, and MiSeq instruments and Pacific Biosciences Single Molecule Real-Time Sequencing on the new Revio platform. In addition, GENSR offers full-service genotyping and methylation analyses using Illumina arrays and reduced representational bisulfite sequencing on Illumina sequencers. The Oxford Nanopore Technologies PromethION platform enables long-read whole genome sequencing, providing resolution of hard to sequence repetitive gene regions, including allele specific telomere lengths, phasing, methylation and focused enrichment of defined genomic regions through adaptive sampling. The Mayo Clinic Spatial Biology component of GENSR was established at MCF in 2019 under the direction of E. Aubrey Thompson (ACTS, MCF). The facility is designed to provide spatial biology analytical resources, on a collaborative basis, to Mayo Clinic investigators. The facility relies primarily on NanoString technology to enable investigators to quantify spatial distribution of both RNA and protein and to carry out single-cell spatial transcriptome and proteome profiling of clinical samples and mouse models of cancer. There is a well-developed cooperative administrative structure that oversees activities and ensures timely access and affordable pricing to MCCCC members, who make up about 40% of the GENSR customer base. All GENSR activities are data intensive. GENSR interacts closely with Information Technology (IT) and Bioinformatics Share Resource (BISR) resources to meet user needs from project inception through the final delivery of data. Member Utilization 2019-2023: 216 Total (8 CPCS, 20 REDI, 45 CGSM, 44 CII, 41 NTTM, 58 ACTS) Publication by Members: 165, 60 with Impact Factor >10