With the ability to help solve many mysteries of disease processes – particularly cancer – RNA sequencing (RNA-seq) technology is a highly valuable tool for biomedical researchers seeking to determine the mutations that cause disease and identify potential sources for drug targets. To date, many genomic labs have operated massively parallel genomic sequencers (also known as NextGen sequencers) using a wide variety of platforms, protocols, and performance capabilities, and that, says Scott Tighe, manager of the NextGen sequencing core at the Vermont Cancer Center’s Advanced Genome Technologies Facility, has created the need for comprehensive analysis of all platforms and establishment of publicly available reference standard data.
In a study co-authored by Tighe and colleagues in an advance online publication in the journal Nature Biotechnology, a group of 21 labs and 60 analytical contributors evaluated and benchmarked every genome sequencer used for sequencing RNA today.
“Our primary goal was to understand the strengths, weaknesses, and variables within each genetic platform including the one we have at UVM,” says Tighe, who is co-chair of the Association of Biomolecular Research Facilities (ABRF) Next Generation Sequencing consortium and chairs its Metagenomics Research Group. ABRF members designed and conducted this first phase of a large-scale next-generation sequencing study.
The publication of Tighe and colleagues’ paper coincides with another topically related paper from the U.S. Food and Drug Administration’s Sequencing Quality Control Project in the same issue. In addition, the ABRF group designed – with the help of an artist – the cover art for the hard copy edition of the September 2014 issue, due out soon.
The momentum fueled by this work has prompted several other activities, including a GenomeWeb webinar on Monday, September 29, 2014, at 12:00 pm EDT, titled “The ABRF-NGS Study: A Multi-Platform Assessment of Transcriptome Profiling by RNA-Seq,” and the launch of a Phase 2 study that will characterize the current inventory of genomic sequencing platforms used for DNA-Seq with complex human DNA standards from NIST (National Institute of Standards and Technology) and its Genome-in-a-Bottle Consortium (GiaB); FFPE (formalin-fixed paraffin-embedded) -derived genomic DNA – common biological materials designed to mimic clinical specimens for disease diagnosis and scientific research; and several bacterial genomes. The Phase 2 study is expected to be completed in late 2016.
View the advance online publication in Nature Biotechnology.