Next Generation Sequencing Shared Resource

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NEXT GENERATION SEQUENCING SHARED RESOURCE (NGS-SR): ABSTRACT The Next Generation Sequencing Shared Resource (NGS-SR) provides the University of Florida Health Cancer Center (UFHCC) members with access to centralized, state-of-the-art, cost-effective next generation sequencing services to advance cancer research. The NGS-SR is an institutionally-managed shared resource supported by UFHCC through a partnership with the UF Interdisciplinary Center for Biotechnology Research, a campus-wide shared biotechnology resource. Located within the Cancer & Genetics Research Complex providing convenient access for UFHCC members, NGS-SR includes 4 staff members under the supervision of Moraga, who has over 30 years of experience in DNA sequencing technologies. During the recent COVID-19 pandemic, the NGS-SR was identified as an essential campus resource and remained staffed and open to the UF research community. NGS-SR service requests and invoicing are managed via the CrossLab laboratory management system. Key sequencing technologies available include instruments from Illumina (NovaSeq6000, MiSeq), PacBio SEQUEL IIe, Oxford Nanopore PromethION, and the 10x Genomics Chromium single-cell RNA-Seq and VISIUM spatial transcriptomics platforms. Raw sequencing read data are directly transferred to the HiPerGator high- performance computing cluster for downstream bioinformatics analysis. UFHCC investments in instrumentation include the Illumina NovaSeq6000, PacBio SEQUEL IIe, mosquito® liquid handling robot, and 10x Genomics Chromium single cell platform. The NGS-SR works in collaboration with the UFHCC Biostatistics and Quantitative Sciences Shared Resource to provide no cost consultation in effective experimental design and best practices in computational analysis of large-scale multi-omic data sets. NGS-SR supports studies in DNA structural and gene variant analysis, microbiome and metagenome analysis, bulk and single cell ATAC-Seq and RNA-Seq, ChIP-Seq, and whole genome sequencing. Since 2016, 54 unique members have used NGS-SR, of which 45 have peer-reviewed funding. There has been an increase in the number of members using NGS-SR each year and an increase in sequencing runs, supporting 54 peer-reviewed publications, with 24% having IF >10. Mechanisms of Oncogenesis and the Cancer Therapeutics and Host Response members represent major users. The effectiveness of the NGS-SR in meeting member needs is assessed by annual surveys, feedback from the NGS-SR Scientific Advisory Group, and recommendations from the Shared Resources Oversight Committee. In response to user requests for lower costs, the acquisition of the NovaSeq6000 reduced sequencing costs by 50% and the use of robotics has reduced RNA-Seq library prep costs by 75%. In alignment with the UFHCC Strategic Plan, Momentum 2027, the demand for NGS-SR services is anticipated to grow with recruitments in molecular epidemiology, immunobiology, and RNA epigenetics. In response, NGS-SR will continue to lower costs through increased automation, expand services including spatial transcriptomics, and adopt new technologies to increase capabilities in cost effective single cell transcriptomics.