Genomics

Our Mission

The mission of the UAMS Genomics Core is to provide UAMS investigators with convenient access to the latest technologies for Next Generation Sequencing (NGS), microarray, and analytical approaches for the evaluation of bio-molecules, eg, nucleic acids.  It is fully supported by the Cancer Institute. 

The specific aims are:

1. provide state-of-the-art genomics technologies in order to generate high-quality data with efficient turn-around time and affordable cost;
2. provide Cancer Institute members with dedicated personnel for time with consultation and technical assistance, in support of experimental design, sample preparation, data acquisition, and initial analysis;
3. maintain state-of-the-art genomics capabilities as well as identify and develop new applications of molecular profiling to advance research within the Cancer Institute.

Overview of Services

Salient services provided for molecular profiling include the complete NGS service, which consists of:

1. sample preparation with QA/QC validation,
2. running the sample 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 file) delivered to the customer.  

Examples of NGS approaches

1. for DNA include:
   • whole-exome
   • whole genome
   • targeted cancer panels. 
2. RNA approaches include:
   • mRNA,
   • total RNA for gene expression,
   • isoform expression,
   • expressed mutations,
   • fusion analysis. 
3. Methylation approaches currently utilize the Infinium EPIC array.  RRBS to be offered soon.

Additional Services Offered

Illumina Bead Array

• MethylationEPIC array for standard or FFPE DNA
• Tecan Freedom EVO for high-throughput array staining
• iScan and Autoloader for high-throughput array scanning

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)
• Targeted DNA panels
• RNA-seq with Truseq Stranded Total RNA
• RNA-seq with Truseq Stranded mRNA
• RNA-seq with Takara SMARTer Stranded Total RNA
• single-cell RNA-seq with 10X Genomics

QC for Nucleic Acids and NGS Libraries

• Qubit fluorometer
• NanoDrop spectrophotometer
• Agilent Fragment Analyzer capillary elctrophoresis system
• Library functional assessment with QuantStudio5 qPCR system

Droplet Digital PCR (ddPCR)

• BioRad QX200 system

DNA Fragment Size Selection

• Sage Science PippinHT

Technology and Instrumentation

NGS Instrumentation

• Illumina HiSeq 3000
• Illumina NextSeq 500
• Illumina miniSeq

Other Molecular Profiling

• Illumina iScan Microarray System with autoloader
• BioRad ddPCR QX200
• 10x Chromium System

Support Equipment

• Advanced Analytical Fragment Analyzer
• Tecan Freedom Evo Robot
• QuantStudio 5 Real Time PCR System
• Sage Science PippinHT