Genomics Shared Resource

Donald Johann, Jr., MD, MSc, FACP

Genomics Shared Resource Director

Johann is a Professor of Biomedical Informatics in the UAMS College of Medicine and serves as the inaugural Director of the Genomics Shared Resource. Johann is a physician-scientist and medical oncologist who trained and was an investigator at the National Cancer Institute in Bethesda, Maryland prior to joining UAMS. Before attending medical school at Case Western University, he worked as an engineering group leader in advanced avionics for the Sperry/Unisys Corporation for seven years and earned a graduate degree in computer science.

• Bing Guan, PhD, Operations Manager – Guan has over ten years of experience in the field of molecular biology, laboratory science, and management. She has a PhD in biochemistry from the Chinese University of Hong Kong, School of Biomedical Sciences.
• Winifred Middleton, MS, Scientific Lead for Wet Lab Operations – Middleton has a broad background in cell and molecular biology, including NGS sample prep. She earned her graduate degree in individualized genomics and health from Johns Hopkins University.
• Other Personnel – Three research associates and two bioinformaticians.

The Genomics Shared Resource provides critically important services to Winthrop P. Rockefeller Cancer Institute investigators. The Shared Resource utilizes state-of-the-art methodologies and technologies to assist users from initial discussions involving experimental design, through sample prep, NGS data generation, and complex bioinformatic analyses. A formal consultation, which is “charge-free,” is required for all new investigators and is focused on the principal investigator’s scientific question and their intended goal, experimental design, budget, and schedule or time constraints.

The Genomics Shared Resource provides Winthrop P. Rockefeller Cancer Institute investigators with cutting-edge technologies for NGS, microarray analysis, and advanced biomolecular evaluation.

Genomics Related Instrumentation

NGS instrumentation includes Illumina NovaSeq X-Plus, NovaSeq 6000, NextSeq 2000, miniSeq, and two iSeq 100 desktop instruments. For sample preparation, equipment includes a Fragment Analyzer^TM by Agilent, Covaris S220 focused ultrasonicator, Qubit^TM, QuantStudio 5 Real-Time PCR System, and a variety of other molecular biology instrumentation. Additionally, the Genomics Shared Resource has a Bio-Rad QX200 droplet digital PCR (ddPCR) system and a Perkin Elmer Sciclone^® G3 NGS and NGSx Liquid Handling and Sample Prep Robot and workstation, which is utilized for DNA and bulk RNA-seq projects. The 10X Genomics single-cell RNA-seq (scRNA-seq) assay is fully supported from cell viability assessment, through sample prep, library generation, and bioinformatics analyses. The associated 10x instrumentation includes Chromium Controller, Chromium X, and the Chromium Connect sample prep robot for advanced robotic automation. 10x cell viability assays utilize a Thermo Fisher Scientific EVOS M7000 microscope that has dual-color imaging with 4′,6-diamidino-2-phenylindole (DAPI) and GFP/RFP, per our custom-developed 10x/Thermo cell viability protocol. The 10x CytAssist Robot is employed for 10x Visium Spatial Transcriptomics assays that are fully supported from sample prep through complex bioinformatics. The 10x Flex single-cell assay is now available for formalin-fixed, paraffin-embedded samples. The Illumina PIPSeq_v5 is also available for single-cell assays involving fresh tissue.

High-Performance Computing

All bioinformatic pipelines utilize the Illumina Dynamic Read Analysis for GENomics (DRAGEN)™ Field Programmable Gate Array (FPGA) methodology, enhancing speed, accuracy, and precision of analyses. We also continue to support NGS and other molecular profiling modalities that utilize computation and storage resources at UAMS, Google Cloud, and on-campus facilities. In 2014, a HIPPA Business Associate Agreement was established between UAMS and Google for utilization of Google Cloud computation services related to the processing of NGS data. The Genomics Shared Resource also has access to a high-performance computing cluster at UAMS. The system consists of ~3,000 Xeon cores, ~6,000 Xeon Phi cores, ~27,000 CUDA cores, ~50 TB memory, 1.9 PB of scratch disk space, and ~1.8 PB of long-term storage disk space via our Synology SA3600 and HD6500 systems which utilize geographic redundancy.

• Bioinformatic Pipelines – State-of-the-art bioinformatic pipelines and downstream analyses have been developed in-house using DRAGEN-based methodology and open-source software. All DNA and RNA NGS bioinformatic pipelines follow best practices established by the Broad Institute of Harvard. Included are pipelines for whole-genome sequencing, whole-exome sequencing, DNA panels with and without the use of universal molecular identifiers, and a variety of RNA pipelines for gene expression analysis, isoform expression, expressed mutations, and fusions. Reduced representation bisulfite sequencing (RRBS) assays are available for epigenetic analyses. Ultra-low-pass DNA copy number analysis is also available. A custom database, the Molecular Profiling Database (MPDB), was designed by Johann and implemented by the Genomics Shared Resource technical staff using the Microsoft SQL Server. For every user project, the MPDB tracks and captures all aspects of the project involving kits and catalog numbers of all reagents, instruments, including NGS, bioinformatics pipelines and tools, and the molecular profiling data. The MPDB has been enhanced with a number of report generation functions allowing for rapid QA/QC analysis of molecular profiling data and generations of detailed molecular profiling reports (e.g., mutational analysis, gene expression analysis, and chromosomal and copy number analyses). Suites of secondary and tertiary tools have been developed for implementing approaches for exploratory data analysis, unsupervised analyses, and statistical inferencing of the molecular profiling data and are available as a Genomics Shared Resource additional service.
• Support Equipment – Three separate but contiguous laboratory bays are utilized by the Genomics Shared Resource. The first bay serves as a pre-PCR lab and contains the following equipment: -80o C freezer, -20o C freezer, 4° C refrigerator, laminar-flow biosafety cabinet, chemical safety hood, Leica microtome, and water bath. The second bay is a post-PCR lab and contains a -20° C freezer, 4° C refrigerator, the Thermo Savant SpeedVac vacuum concentrator, and the Perkin Elmer Sciclone® G3 NGS and NGSx liquid handling and sample prep robot and workstation. The third bay serves as the sequencing and analysis lab, housing all NGS instrumentation and other analytical equipment.