Shared Resource Spotlight: NextGen DNA Sequencing
Everything You Need to Know About This ICBR Shared Resource
Ben Hoffman, Core Research Technician III, Diansy Zincke, Ph.D., Xiao Hui Zhou, Core Research Technician III, David Moraga, Ph.D.
The mission of the NextGen DNA Sequencing is to provide easy access to cost-effective, high-throughput sequencing services encompassing a broad range of applications for biological research including RNA transcriptome analysis, targeted genome and variant analysis, microbiome analysis, epigenetics and de novo genome assembly.
A partnership between the UF Health Cancer Center and the UF Interdisciplinary Center for Biotechnology Research (ICBR), the NextGen DNA Sequencing shared resource provides Cancer Center members access to state-of-the-art instrumentation, and scientific and technical expertise for conducting impactful genomic-based research studies in support of the strategic aims of basic translational and clinical cancer research activities.
Below, Director David Moraga, Ph.D., gives us an inside look at the shared resource’s services, aims and training opportunities — and explains why YOU should consider using this resource for future research.
What’s important for Cancer Center members to know about the NextGen DNA Sequencing shared resource?
Xiao Hui Zhou, NextGen Core Technician III operating new PacBio Sequel IIe
The NextGen DNA Sequencing shared resource provides expertise and cutting-edge instrumentation in two types of technologies — short-read DNA fragment sequencing on the Illumnia platform and long-read sequencing on the PacBio SEQUEL instrument. We are also in the process of bringing the Oxford Nanopore Technology PromethION instrument online, which can generate very long DNA reads and analyze RNA in its native form.
We further offer free consultation to members for effective planning and experimental design to be sure members are utilizing the correct sequencing approaches for their research. We welcome interaction with members to optimize protocols for processing samples. Our list of services is evolving due to our response to the needs and feedback of our members.
What services does NextGen DNA Sequencing offer and why should our members utilize them?
Diansy Zincke, Ph.D., NextGen Core Facility Specialist II working on the Illumina NovaSeq 6000
The NextGen DNA Sequencing shared resource offers the latest sequencing instrumentation for the two most utilized platforms: Illumina and PacBio. We offer cost-effective library construction services for some of the most common sequencing applications.
We use optimized and validated protocols with rigorous QC in order to ensure the best possible data quality. Since UF Health Cancer Center members get a 20% reimbursement for all invoices from the NGS-SR, fees for our services are extremely competitive.
What is a particularly notable service that you want to make sure members are aware of?
Setting-up a long-read sequencing run on the Sequel IIe
The PacBio SEQUEL IIe platform is a powerful and useful technology that represents untapped potential for many cancer-relevant applications. This includes the mRNA splice variant analysis, non-coding RNA detection and identification of gene structural variants. The PacBio SEQUEL instrument is capable of generating single read lengths averaging up to 60 kilo bases.
What is the relationship between NextGen DNA Sequencing and our other shared resources?
UF Health Cancer Center members can use all cores in isolation as each core operates independently. However, we believe that there are significant benefits that can be realized in the form of increased rigor and reproducibility by using the core resources in an integrated fashion.
Cancer Center members benefit from having access to not only the NextGen DNA Sequencing, Biostatistics & Quantitative Sciences and Flow Cytometry and Confocal Microscopy shared resources, but also to five other core technologies in the ICBR: Proteomics and Mass Spectrometry, Monoclonal Antibodies, Electron Microscopy, Gene Expression and Bioinformatics. The ICBR is organized such that projects requiring multi-core expertise are readily planned and completed by coordinated efforts amongst each core staff.
An example is with single cell RNASeq; tumor cells can be isolated in the Cytometry SR, delivered to the ICBR Gene Expression Core for library preparation and then sent to Next Generation Sequencing for analysis. The final batch of raw sequencing data is securely delivered to BQS for analysis. This process is guided by strict SOPs to ensure rigor and reproducibility.
What are some examples of cancer-related, NextGen DNA Sequencing-Assisted Research at UF?
Xiao Hui Zhou, NextGen Core Technician III unpacking SMRTcells for a SEQUEL IIe run
Hardly a week goes by without processing Cancer Center members’ samples that require services related to quality control, library construction and sequencing.
We have recently processed several RNAseq and ATACseq experiments from Dr. Jonathan Licht’s lab that aimed to evaluate the relationship between gene expression patterns and histone accessibility. We are also processing samples from Dr. Rolf Renne from a pilot study that aims to identify novel micro-RNAs that may be involved in various cancer malignancies.
What do you enjoy about your role as the Director of NextGen DNA Sequencing?
David Moraga, Ph.D. NextGen Core Director operating the Illumina MiSeq
I enjoy my daily interaction with dedicated scientists who are trying to not only understand the basic molecular and cellular basis for cancer, but also discover novel and effective therapies that will benefit patients. It is satisfying to know that the work of our core plays a role in supporting and enabling the progress that is being made.
