Genomics

The Genomics Shared Resource provides UAMS investigators with convenient access to the latest technologies for next generation sequencing (NGS) and analytical approaches for the evaluation of biomolecules.

Contact

For questions and service requests, please contact Bing Guan, Operations Manager, at BGuan@uams.edu , or Dr. Donald Johann, Director, at DJJohann@uams.edu.

Overview

Services provided for molecular profiling include:

1. Tissue/sample preparation with QA/QC validation;
2. Running samples on the NGS instrument;
3. Bioinformatics pipeline processing, specifically QA/QC analysis of NGS data, sequencing data alignment, molecular characterization of mutational findings, report generation (annotated Excel files) delivered to the customer, exploratory data analysis (EDA), and unsupervised advanced clustering analysis of RNA-seq biological replicates. Delivered data is ready for biological pathway analysis via IPA, DAVID, etc.; and
4. Data storage for a period of seven (7) years, including NGS data, such as FASTQ, BAM, VCF and associated files. Our custom database also captures all method-related data pertaining to sample prep kits, catalog numbers, etc., as well as all technical details and methods associated with bioinformatics.

NGS Approaches

DNA: Whole Exome Sequencing (WES); Whole Genome Sequencing (WGS); Targeted Cancer Panel, 558 genes based on TCGA findings, tumor agnostic, matched DNA and RNA (558 each), utilizing Universal Molecular Identifiers (UMIs) to reduce false positives; and liquid biopsy assays for somatic mutational analysis, clonal hematopoiesis of an indeterminant potential (CHIP), methylation analysis, fragmentomics analysis.

RNA: mRNA; total RNA; targeted panel (558 cancer genes); isoform expression; expressed mutations; and fusion analysis. 

Methylation: Reduced Representation Bisulfite Sequencing (RRBS); Whole Genome Bisulfite Sequencing (WGBS); and enzymatic-based methylation sequencing for whole genome and targeted panels.

Services

Nucleic Acid Extraction

• DNA & RNA from cells, solid tissues, & FFPE
• cfDNA from plasma & urine

NGS Library Preparation

• Whole Genome including low-pass or ultra-low-pass (0.1 – 0.3x)
• Whole Exome Sequencing
• Targeted DNA and matching RNA panels with UMIs (558 genes)
• Bulk RNA-seq using Total RNA
• Bulk RNA-seq using mRNA
• RRBS, WGBS
• Enzymatic-based methylation via whole genome or panel
• 10x single-cell RNA-seq for 3’ or 5’ gene expression
• 10x Visium Spatial Transcriptomics via CytAssist for FFPE specimens
  • High definition using 6.5 mm² FFPE tissue sections
  • Standard resolution using either 6.5 mm² or 11 mm² FFPE tissue sections

QC for Nucleic Acids and NGS Libraries

• Qubit fluorometer for nucleic acid quantification
• NanoDrop spectrophotometer
• Agilent Fragment Analyzer capillary electrophoresis system
• Library functional assessment with QuantStudio5 System via qPCR

Droplet Digital PCR (ddPCR)

• BioRad QX200 system

DNA Fragment Size Selection and Analysis

• Sage Science PippinHT

Technology and Instrumentation

NGS Instrumentation

• Illumina NovaSeq 6000
• Illumina NextSeq 2000
• Illumina miniSeq
• Illumina iSeq

Other Instrumentation Supporting Molecular Profiling Tasks

• 10x Chromium Controller
• 10x Chromium X System
• 10x Chromium Connect Robot for scRNA-seq assays
• BioRad ddPCR QX200
• Sciclone G3 NGSx Liquid Handler and Sample Prep Robot for bulk RNA and DNA assays.

Equipment

• Advanced Analytical (now Agilent) Fragment Analyzer
• QuantStudio 5 Real Time PCR System
• Thermo Fisher Scientific EVOS M7000 Microscope, used for cell viability assays as part of the 10x Genomics Single Cell assay.