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 sequencing technology has become the most widely adopted next-generation sequencing platform. 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 three types of Illumina sequencers: MiSeq, HiSeq 2500, and HiSeq 4000. A single 3.5 day HiSeq 4000 run can generate sufficient data to sequence 12 human genomes, more than 150 human exomes, up to 100 human transcriptomes, or thousands of microbial genomes. The MiSeq platform offers longer reads and more rapid turnaround time with lower overall throughput. Typical applications for our MiSeq platform include microbial genome sequencing, amplicon sequencing, and customized sequencing panels.
Pacific Biosciences (PacBio) 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.
The GRC is a PacBio Certified Service Provider and operates both the PacBio RS II and the newer Sequel System. 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 de novo genome sequencing, variant detection and validation, methylation analysis, targeted/amplicon sequencing, and full-length transcript sequencing (Iso-Seq).
The NanoString nCounter Analysis System has the ability to digitally quantify changes in up to 800 DNA, RNA, and protein targets using a single detector from samples of limited volume and concentration without the need for amplification or library preparation. The nCounter’s digital counting capability provides highly reproducible data over 5 logs of dynamic range and does not require any amplification steps that might introduce bias to the results. An additional advantage of nCounter chemistry is that it is highly tolerant of difficult sample types such as FFPE and crude-cell lysates. With a technology that expands our capabilities and complements our high-throughput sequencing platforms, we are excited to have the NanoString nCounter join our growing family of services.
Oxford Nanopore MinION
The Oxford Nanopore MinION is the world’s first nanopore DNA sequencer. It is a portable, low-cost, long-read sequencing device that may prove disruptive to the sequencing landscape. The GRC is part of the MinION Early Access Programme and is currently evaluating this technology.