title: Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.
abstract: High-throughput RNA sequencing (RNA-seq) greatly expands the potential for genomics discoveries, but the wide variety of platforms, protocols and performance capabilitites has created the need for comprehensive reference data. Here we describe the Association of Biomolecular Resource Facilities next-generation sequencing (ABRF-NGS) study on RNA-seq. We carried out replicate experiments across 15 laboratory sites using reference RNA standards to test four protocols (poly-A-selected, ribo-depleted, size-selected and degraded) on five sequencing platforms (Illumina HiSeq, Life Technologies PGM and Proton, Pacific Biosciences RS and Roche 454). The results show high intraplatform (Spearman rank R > 0.86) and inter-platform (R > 0.83) concordance for expression measures across the deep-count platforms, but highly variable efficiency and cost for splice junction and variant detection between all platforms. For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA depletion enables effective analysis of degraded RNA samples. This study provides a broad foundation for cross-platform standardization, evaluation and improvement of RNA-seq.
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.|The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
authors.forename: Sheng
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authors.lastname: Li
authors.affiliation: Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA.
authors.forename: Scott W
authors.initials: SW
authors.lastname: Tighe
authors.affiliation: Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
authors.forename: Charles M
authors.initials: CM
authors.lastname: Nicolet
authors.affiliation: The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.
authors.forename: Deborah
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authors.lastname: Grove
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
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authors.affiliation: Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA.
authors.forename: William
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authors.affiliation: Memorial Sloan-Kettering Cancer Institute, New York, New York, USA.
authors.forename: Agnes
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authors.affiliation: Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois, USA.
authors.forename: Chris
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authors.affiliation: Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Schweitzer
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
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authors.lastname: Gao
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Dewey
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authors.affiliation: NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA.
authors.forename: Joe
authors.initials: J
authors.lastname: Boland
authors.affiliation: NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA.
authors.forename: Belynda
authors.initials: B
authors.lastname: Hicks
authors.affiliation: Genome Center, University of California, Davis, Davis, California, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Kim
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.|The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
authors.forename: Sagar
authors.initials: S
authors.lastname: Chhangawala
authors.affiliation: Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA.
authors.forename: Nadereh
authors.initials: N
authors.lastname: Jafari
authors.affiliation: NIH/NHLBI, Bethesda, Maryland, USA.
authors.forename: Nalini
authors.initials: N
authors.lastname: Raghavachari
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.|The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
authors.forename: Jorge
authors.initials: J
authors.lastname: Gandara
authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi, USA.
authors.forename: Natàlia
authors.initials: N
authors.lastname: Garcia-Reyero
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Hendrickson
authors.affiliation: NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA.
authors.forename: David
authors.initials: D
authors.lastname: Roberson
authors.affiliation: Division of High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Rosenfeld
authors.affiliation: PerkinElmer Inc., Seattle, Washington, USA.
authors.forename: Todd
authors.initials: T
authors.lastname: Smith
authors.affiliation: University of Washington, Department of Genome Sciences. Seattle, Washington, USA.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Underwood
authors.affiliation: Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA.
authors.forename: May
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.|The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Zumbo
authors.affiliation: Pathonomics LLC, Philadelphia, Pennsylvania, USA.
authors.forename: Don A
authors.initials: DA
authors.lastname: Baldwin
authors.affiliation: Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA.
authors.forename: George S
authors.initials: GS
authors.lastname: Grills
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.|The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
mesh_terms: D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D059467:Transcriptome