Genomics Resource Center - Platforms

The GRC occupies custom-designed BSL-2 research space within the University of Maryland BioPark II facility. The GRC has equipped the laboratory with custom-built laboratory automation platforms to increase efficiency, reduce error, and increase throughput. We utilize a customized Laboratory Information Management System (LIMS) for reagent, sample, and project tracking. The GRC LIMS increases efficiency and reduces errors through the use of custom workflows for each platform. These workflows provide process control and validation to ensure each sample is processed according to established and reviewed protocols. Our custom-designed facility, automation platforms, and LIMS support our high-throughput sequencing pipelines.

Illumina

Illumina sequencing technology has become the most widely adopted next-generation sequencing platform and forms the base of the GRC sequencing operations. Illumina sequencers provide high-throughput, short-read sequence data with the lowest cost-per-base of any commercially available platform. The technology uses sequencing-by-synthesis on a glass surface (flowcell) to produce billions of reads per run with read lengths up to 300bp and growing. This platform enables many applications, including whole genome sequencing, exome and custom targeted sequencing, transcriptome sequencing, epigenomic sequencing, and others. The GRC operates two types of Illumina sequencers.

HiSeq4000 & HiSeq2500

Our Illumina HiSeq sequencers represent the highest throughput platform currently available. A single 3.5 day HiSeq 4000 run can generate sufficient data to sequence any of the following:

  • Twelve human genomes
  • More than 150 human exomes
  • Up to 100 human transcriptomes
  • Thousands of bacterial genomes
  • Thousands of viral genomes
  • And many others!
hiseq

MiSeq & MiSeq Dx

The Illumina MiSeq platform uses the same trusted chemisty as the HiSeq, but offers longer reads and more rapid turnaround time with lower overall throughput. Typical applications for our MiSeq platform include:

  • Targeted capture sequencing
  • Microbial genome sequencing
    • Outbreak response
    • Small sample size
  • Amplicon sequencing
    • 16S profiling
    • Variant validations
    • Large-scale genotyping
  • Clinical sequencing panels
miseq

Pacific Biosciences

The Pacific Biosciences RS II is a single-molecule, real-time (SMRT) sequencing technology capable of detecting signal from an individual DNA molecule coupled with an individual DNA polymerase. It achieves the highest consensus accuracy and longest read lengths of any currently available sequencing technology and is free of amplification artifacts that can confound other sequencing technologies. While lower overall throughput than other technologies is a limitation with this platform, the fundamentally stochastic and unbiased error profile leads to rapid increases in accuracy as sequencing coverage increases.

With a mean read length greater than 10,000 bases, more than half of the reads exceeding 14,000 bases on many runs, and a maximum read length >50,000 bases, the platform enables many applications not possible with other technologies. The reaction kinetics data that are detected during the run can be used to natively detect modified nucleotides for epigenomic applications. Some applications ideally suited for this platform include:

PacBio
  • de novo genome sequencing (resulting in complete or nearly complete genomes for many organisms)
  • variant detection & validation
  • epigenomic sequencing (base modification detection)
  • indel & structural variation detection & validation
  • targeted sequencing & haplotype phasing
  • full-length transcript sequencing
Pac Bio certified service provider

Sanger capillary sequencing

Applied Biosystems capillary electrophoresis sequencers generate up to 1000bp reads, but at a lower throughput and higher cost compared to newer platforms. Though using an older technology, this Sanger-based platform remains the platform of choice for small-scale applications, PCR-based variant validations, and small projects requiring longer read lengths.