By Julia Karow
The Association of Biomolecular Resource Facilities has launched a long-term study of next-generation sequencing platforms and plans to present the project design, as well as some "very preliminary" results from its first phase, at its annual meeting in Orlando, Fla., next week.
The aim of the ABRF-NGS study is to assess the technical performance of next-generation sequencing platforms for DNA and RNA analysis. The study is a joint effort of five of the organization's research groups, which focus on DNA sequencing, genomic variation, nucleic acids, microarray research, and genomics bioinformatics.
The study's first project is focusing on transcriptome analysis and will assess sequencing accuracy, absolute and relative expression levels, and differential expression for four next-generation sequencing platforms, according to the ABRF website.
The study runs in parallel to the Food and Drug Administration's Sequencing Quality Control, or SEQC, study, a follow-on project to the MicroArray Quality Control Consortium study, and some laboratories are participating in both efforts (IS 11/29/2011).
While both studies have similar goals in terms of assessing the performance of next-gen sequencing platforms for transcriptome sequencing, the ABRF study will include newer technologies and other types of protocols, and has a different long-term goal: the creation of a community resource-type database where researchers can upload their own sequencing results anonymously and compare them with those of others. This resource will be modeled on a similar one that the ABRF DNA research group once built for users of Sanger sequencing technology.
"We're really looking at this as a model for core labs and other investigators to evaluate technologies," said George Grills, director of operations of life sciences core facilities at Cornell University and a project coordinator of the ABRF-NGS study. Grills added that next-generation sequencing technologies are developing so rapidly "that any publication is just a snapshot of the rapidly moving field."
"We all have a rich appreciation for how fast the field moves, but at the same time, with no good benchmarks to compare within a platform, you have no idea what's different between one release of the chemistry [or another], or a different protocol, or how much degradation matters for what you're trying to measure," said Christopher Mason, an assistant professor in the department of physiology and biophysics at Weill Cornell Medical College and the scientific lead for the ABRF study.
"Our big concern is that you can't take the same genome and sequence it and get the same answer twice," Mason added. "And you need to be able to do that if we are ever going to branch deeply into the clinical realm." Mason is also involved with the FDA-SEQC study.
The study is not intended to be a "bake-off" between platforms, though. "The different platforms have different sweet spots in terms of their most ideal applications," said Grills, and even though they do compete commercially to some extent, the study is "not focusing on that."
For its initial project, the ABRF-NGS study is assessing the Illumina HiSeq 2000, the Ion Torrent PGM, the Roche/454 FLX+ system, and the PacBio RS.
It will use the same RNA reference samples that the MAQC study used several years ago to evaluate the performance of array platforms, as well as spike-in controls that were originally developed by the External RNA Controls Consortium.
At least three labs will assess each platform, using the same protocols and standard operating procedures. A bioinformatics and bio-IT group will analyze the data and eventually build the community resource where results can be posted, which the study plans to have in place by next year.
By this fall, the study participants hope to submit their results to a journal for publication, most likely Nature Biotechnology, where MAQC has published its results.
Following that, they plan to tackle the second phase of the project, which will assess the sequencing platforms for a number of other applications, such as sequencing of degraded RNA and DNA, microRNA sequencing, sequencing of HapMap trios, and analysis of DNA templates with difficult-to-sequence regions. Preliminary results are already in hand for some of these applications, Mason said.
Funding for the study comes from several sequencing instrument vendors, the labs of participating ABRF laboratories, and from ABRF itself, and the organizers are in discussions with other vendors for additional support. In addition, they are in talks with federal grant agencies as well as bioinformatics companies about funding for the community resource.
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