Shared Resources
The UF Health Cancer Center strives to provide cancer scientists with state-of-the-art technology and expertise to foster and facilitate outstanding cancer research.
Flow Cytometry and Confocal Microscopy Shared Resource (CYT-SR)
Director:
Andria Doty, Ph.D.
Mission:
The mission of the Flow Cytometry and Confocal Microscopy Shared Resource (CYT-SR) is to provide UF Health Cancer Center members with easy access to cost- effective, leading-edge cytometry instrumentation, novel methodologies and data analysis expertise, and facilitate instrument self-use through comprehensive user training.
Program Aims:
- Provide access to cost effective, state-of-the-art flow cytometry analysis and sorting and live cell confocal microscopy services.
- Provide training leading to certification in self-use of flow and confocal microscopy instruments.
- Provide consultation on experiment design, assistance with data interpretation and support for scientific publications and research grant applications.
- Identify and evaluate new instrumentation and ensure alignment of instrument capabilities with user needs based upon end-user and faculty surveys and recommendations from the CYT-SR Scientific Advisory Group.
Major Services:
- Multi-parameter flow cytometry
- Confocal microscopy with live cell imaging
- Microparticle analysis n Expert consultations in experiment design and preparation of research grant applications
- Instrument training, courses and workshops
Next Generation Sequencing Shared Resource (NGS-SR)
Director:
David Moraga, Ph.D.
Mission:
The mission of the Next Generation Sequencing Shared Resource (NGS-SR) is to provide members with easy access to cost-effective state-of-the-art NGS services to support research activities.
Program Aims:
- Provide ready access to cost-effective, state-of-the-art next-generation sequencing technologies and instrumentation as well as highly skilled technical staff to support research programs.
- Provide expert consultation on effective use of NGS technologies, assistance with data interpretation, and support for scientific publications and research grant applications.
- Ensure rigor and reproducibility of all research conducted at NGS-SR through the use of standard operating procedures, continuous staff training, monitoring instrument performance metrics, and appropriate data handling, transfer and storage.
- Lead efforts to acquire new instrumentation and develop and validate new methodologies to expand capabilities and expertise in NGS-SR to meet growing demands of membership.
Major Services:
- Massively parallel, high- throughput whole genome sequencing
- Library prep for genomic DNA/exome analysis, epigenetics, microbiome studies and RNA-sequencing
- Expert consultations in effective use of NGS technologies
- Collaboration with the Biostatistics and Quantitative Sciences Shared Resource for streamlined data analysis of large-scale genomic datasets
- Instrument training and workshops
Biostatistics and Quantitative Sciences Shared Resource (BQS-SR)
Director:
Ji-Hyun Lee, DrPH
Mission:
The mission of the Biostatistics and Quantitative Sciences Shared Resource (BQS-SR) is to promote rigorous and reproducible statistical and quantitative sciences for research.
Goal:
The overall objective of the BQS-SR is to provide centralized, leading-edge and accessible collaborative services to ensure scientific rigor in the development and execution of UFHCC cancer research.
Program Aims:
- Provide biostatistical and quantitative services to UFHCC investigators through the three search programs for the design of studies, development of grant proposals, analysis of data, publication, and dissemination of findings.
- Enhance transdisciplinary research and team science through coordination with other SRs and facilitating collaborations among faculty to provide the services described above.
- Support UFHCC clinical trials, including participation in the Scientific Review and Monitoring Committee (SRMC) and the Data Integrity and Safety Committee (DISC), thereby ensuring high quality of science, data integrity, and patient safety in UFHCC clinical cancer research.
- Educate UFHCC faculty, staff, and trainees in current “best practices” and uses of biostatistics, bioinformatics, and computational biology to ensure rigorous and reproducible research.
Major Services:
- Biostatistics Support:
- Conceptualization of a research project, including development of hypotheses; study design, including endpoint selection, sample size justification/power analysis; and analytical planning for research studies.
- Data management, including guidance in the development of study databases, the establishment procedures for monitoring data quality, and the preparation of analysis datasets.
- Reproducible statistical analysis using R markdown/GitHub and SAS macros developed in the BQS-SR which increase the efficiency and integrity of routine statistical analyses as well as reproducibility of the analysis results and report.
- Assistance in grant preparation, manuscript writing, and report generation as required for special studies, such as clinical trials summaries and data and safety monitoring board review.
- Development of statistical methods, tools, or computer programs required to conduct studies, if currently available approaches are insufficient.
- Real time data surveillance for clinical trials, using R shiny app for each UFHCC IITs.
- Bioinformatics/Health Informatics/Computational Biology Support:
- Analysis and annotation of high-throughput genomic assays including RNA-seq, DNA-seq, Chip-seq, ATAC- Seq, bisulfite sequencing, single-cell RNA sequencing, and data from microarray, proteomics, and cytometry.
- Assistance in the development of bioinformatics components of grant proposals, protocols, and manuscripts.
- Development of analysis tools and pipelines for high-performance computing environments.
- Application of machine/deep learning methods to multi-source high-dimensional data.
- Development of mathematical models and user-friendly software to integrate multi-omics platforms.
- Training in biostatistics and bioinformatics through the series of seminars and short courses
- The BQS-SR employs a comprehensive array of technologies and equipment to provide quantitative consultations and collaborations for UFHCC members. These include:
- All necessary statistical software packages, including SAS, R, nQuery, PASS, and SPSS.
- UF state-of-the-art high-performance research computing infrastructure (HiPerGator, a cluster-based 3rd most powerful supercomputer in public universities with > 65K cores, hosting hundreds of bioinformatics packages and > 4 petabytes of ultra-high-performance storage.).
- Genomic analysis software, including Ingenuity Pathway Analysis (IPA).
- Geospatial analysis capabilities through R applications and ArcGIS extensions.
- Leading-edge software for genomic data analysis:
- miTAR: A hybrid deep learning-based approach for predicting miRNA targets
- SCnorm R-Package to normalize single-cell RNA-seq data
- Trendy R-package to perform breakpoint analysis on RNA-seq data
- Next maSigPro Bioconductor package for RNA-seq time series and PaintOmics 3: a web tool for visualization of transcriptomics, metabolomics, and multi-omics data
- Support for Quantitative Training and Education Program:
- Biostatistics 101 (BIOS 101) & Bioinformatics 101 (BIOI 101) for Cancer Researchers: These 8-week courses cover principles of biostatistics and bioinformatics and are targeted to early career researchers or those looking for a refresher on specific topics.
- Biostatistics & Bioinformatics Walk-In Clinic (BB WINC): Weekly provides basic Q&A for biostatistical and bioinformatics topics. The goal of BB WINC is to improve BQS-SR visibility and outreach to cancer-focused laboratory scientists, students, junior faculty and new members of the UFHCC.
In summary, during year 2020, the BQS-SR supported 101 requests from 60 UFHCC members for external grant proposal (28%), investigator-initiated protocol developments (33%), and peer-reviewed publications (21%). Also, the BQS-SR successfully recruited a Bioinformatics faculty, Dr. Jason Brant who has been already working with several UFHCC members.
Developing Shared Resources
Cancer Informatics Shared Resource
Cancer informatics focuses on the development, application, and evaluation of innovative informatics methods, models, and tools with the goal of improving cancer outcomes across the cancer care continuum. The advancement of cancer prevention, diagnostics, and treatments depends on clinical research and quality improvement efforts, as well as translational and broader population research. The Cancer Informatics Shared Resource is equipped to provide expertise and collaboration for investigators across the University of Florida, with a priority on cancer-focused studies.
Gene Editing/CRISPR
CRISPR technology facilitates the precise editing of targeted regions of mammalian genomes and remains one of the key recent advances in biotechnology. The CRISPR technology core offers Cancer Center researchers with access to expertise in Cas9-mediated gene engineering in mammalian cells as well as custom services for CRISPR-based whole-genome phenotypic screens.
Drug Screening
The drug screening core has the capability to run medium-to high-throughput screens (96- and 384-well plate format) and experienced personnel to miniaturize assays. Assay platforms include biochemical assays using colorimetric, fluorescence and ultra-sensitive luminescence outputs including assays designed to quantify protein concentration and protein-protein interactions using the AlphaLISA technology.
