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ABRF Research Groups to Spearhead FDA's Sequence Quality Control Project


By Bernadette Toner

SAN ANTONIO, Texas — Several research groups under the auspices of the Association of Biomolecular Resource Facilities will work with the US Food and Drug Administration to assess the technical performance of next-generation sequencing platforms for DNA and RNA analysis, ABRF officials said this week at the organization's annual conference.

Four ABRF research groups — the Genetic Variation Research Group, the DNA Sequencing Research Group, the Nucleic Acids Research Group, and the Microarray Research Group — will perform the analysis for the Sequence Quality Control project, Michael Zianni, DSRG chair and manager of the Plant-Microbe Genomics Facility at Ohio State University, said during a session at the conference.

The SEQC is a continuation of the Microarray Quality Control project — an initiative that the FDA kicked off in 2005 in an effort to evaluate the reproducibility of microarray platforms. In late 2008, the agency turned its attention to sequencing technologies and issued a solicitation for volunteers to participate in SEQC (IS 1/6/2009).

Christopher Mason, assistant professor at the Institute for Computational Biomedicine at Weill Cornell Medical College, will be the scientific lead for the project. George Grills, director of operations of core facilities at Cornell University and a member of the ABRF executive board, will help coordinate ABRF's involvement in the effort, while the leaders of the four ABRF research groups will bear responsibility for the sequencing and analysis.

Zianni noted that the study is still in the "design stage," but expects to evaluate all platforms currently on the market, including the Illumina GA and HiSeq 2000, SOLiD 4, Roche/454 FLX, Helicos, Ion Torrent PGM, and Pacific Biosciences platforms.

ABRF officials said that the vendors and FDA are providing financial support for the project, including samples and reagents.

The project will initially focus on transcriptome analysis, and the study sites will use the same RNA reference samples that MAQC used for its assessment of microarray platforms, along with spike-in controls developed by the External RNA Controls Consortium.

Samples will be shipped to participating sites next month. By the end of May, the test sites will submit their data to the FDA's National Center for Toxicological Research, which will then ship the data to the analysis sites by the end of June. The goal is to submit a paper for publication by the end of the calendar year, Zianni said.

SEQC participants will assess sequencing accuracy, absolute and relative expression levels, and differential expression.

Zianni and other ABRF officials stressed that the goal of the project is to establish the baseline performance of each platform, which other sequencing groups could use to assess how well their systems and protocols are performing. In another session at the conference, Don Baldwin, co-chair of MARG and director of the Microarray Facility at the University of Pennsylvania, said that SEQC isn't intended to be a "bake-off" that pits different platforms against each other, but rather an effort to establish a reference data set with "truth built in" by analyzing samples with known quantities of RNA.

Likewise, Grills told In Sequence that the goal of the project "isn't benchmarking" of different platforms, but rather an opportunity to offer core labs and other facilities a resource for "self-evaluation and self-improvement."

Grills said that the long-term goal would be an ABRF-managed "community resource" that would allow outside groups to post their own performance data as instruments and protocols change — a key feature given the rapid pace of development in the next-gen sequencing industry. "We want to have the tools in place to enable the evaluation of these technologies as they evolve," he said. "We need to be nimble enough to be able to respond to drastic changes."

He added that the project should highlight what the ABRF research groups "already do well" in terms of impartial evaluation of various technology platforms. The goals of the SEQC project, he said, are aligned with the mission of the research groups, which is to "look at applications and best practices and identify the most optimal ways of using them."

As for the project's aim to generate the data on multiple platforms, analyze it, and publish it before the end of the year, Grills conceded that the timeline is "ambitious," but said he believes it is "doable."

Longer term, the SEQC project aims to carry out a similar study for DNA sequencing, but Grills said that it made sense to start with RNA-seq since the reference samples were already available from MAQC.

Future goals for the effort include DNA and RNA sequencing of a HapMap trio and similar analysis of HeLa cells.

Have topics you'd like to see covered in In Sequence? Contact the editor at btoner [at] genomeweb [.] com.

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