An updated case study about the Genomics Resource Center (GRC) at the University of Maryland’s Institute for Genome Sciences (IGS) reports that SMRT Sequencing has become an integral tool for generating complete microbial genomes, improving plant and animal genome assemblies, and exploring human genome variation.
The GRC has a scientific pedigree and a sample-to-interpretation service commitment that place it in a league of its own. The team operates under a simple mantra: ‘If it can be sequenced, we can do it.’
Both the GRC and IGS were founded in 2007 when a high-powered team of investigators formerly at The Institute for Genomic Research (TIGR), led by Claire Fraser, joined the University of Maryland School of Medicine. “The team of faculty and staff that came here to start the institute was heavily focused on infectious disease research,” says Luke Tallon, scientific director and founding leader of the GRC. “Our primary goal in joining a medical school was to extend our pathogen genomics expertise into host-pathogen studies and direct clinical genomics applications.”
In addition to its infectious disease and genomics expertise, TIGR was also renowned for its bioinformatics talent — a trait that continues with the group at the GRC. Their team of 15 staff members is evenly split between wet lab and bioinformatics, and more than half of the institute’s 100-plus employees are bioinformaticians.
The GRC was formed both to serve the genomics institute and as a university core. “We serve investigators throughout the University of Maryland system as well as across the country and around the world,” says Lisa Sadzewicz, administrative director of the facility. “Our strength is not just our deep history and experience in sequencing and genomics, but our end-to-end service level from the initial project consultation through to publication, including all of the informatics.”
Over the past five years, the GRC has applied these strengths to the PacBio platform. As early adopters of the technology, they have dedicated significant resources to the development of both laboratory and data analysis processes to leverage SMRT Sequencing. Since its adoption of the original PacBio RS in 2011, the GRC has steadily increased its utilization of the platform. In the past year alone, they have constructed more than 400 libraries and sequenced more than 1,200 SMRT Cells. These have spanned projects ranging from whole genome sequencing to metagenomics, Iso-Seq transcriptomes, and custom amplicons.
The GRC’s newest PacBio sequencer arrived in February 2016, making them one of the first PacBio Certified Service Providers to take delivery of a Sequel System. “Given our history of early adoption and success with the PacBio RS, and the promise of increased and scalable throughput, we were excited to be among the first centers to acquire a Sequel instrument,” says Dr. Fraser. The Sequel System represents the newest generation of SMRT Sequencing, providing more scalability and lower sequencing project costs compared to the PacBio RS II.
Development of processes and applications for the Sequel System is well underway at the GRC. The team plans to use the increased throughput to expand their services for Iso-Seq transcriptome sequencing and amplicon projects. In collaboration with Dr. Jacques Ravel, associate director of IGS, they are also developing a full-length 16S sequencing pipeline to complement and expand their human microbiome and metagenomic research portfolios. As read lengths and throughput on the Sequel instrument improve, Tallon’s team will shift whole genome sequencing projects onto the platform.
For other teams considering whether SMRT Sequencing is the right choice for them, Tallon says: “If you value complete genome sequences, de novo transcript discovery, and are looking at epigenetics in addition to the genome sequence, there’s no better technology out there.”
June 10, 2016 | General