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PMID: 25150835 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.

Nature biotechnology ·Vol. 32 ·No. 9 ·2014-09-00 ·Pages 915-925

Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE

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.

MeSH Terms
Gene Expression Profiling High-Throughput Nucleotide Sequencing/methods Transcriptome
Authors & Affiliations
29 authors, click to expand affiliations / ORCID
Li Sheng
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.
Tighe Scott W
Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA.
Nicolet Charles M
Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
Grove Deborah
The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.
Levy Shawn
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Farmerie William
Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA.
Viale Agnes
Memorial Sloan-Kettering Cancer Institute, New York, New York, USA.
Wright Chris
Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois, USA.
Schweitzer Peter A
Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA.
Gao Yuan
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
Kim Dewey
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
Boland Joe
NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA.
Hicks Belynda
NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA.
Kim Ryan
Genome Center, University of California, Davis, Davis, California, USA.
Chhangawala Sagar
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.
Jafari Nadereh
Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA.
Raghavachari Nalini
NIH/NHLBI, Bethesda, Maryland, USA.
Gandara Jorge
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.
Garcia-Reyero Natàlia
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi, USA.
Hendrickson Cynthia
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Roberson David
NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA.
Rosenfeld Jeffrey
Division of High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA.
Smith Todd
PerkinElmer Inc., Seattle, Washington, USA.
Underwood Jason G
University of Washington, Department of Genome Sciences. Seattle, Washington, USA.
Wang May
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA.
Zumbo Paul
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.
Baldwin Don A
Pathonomics LLC, Philadelphia, Pennsylvania, USA.
Grills George S
Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA.
Mason Christopher E
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.
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.2972
Published
2014-09-00
Epub
2014-00-24
Pages
915-925
Language
English
Region
United States
NLM ID
9604648
PMCID
PMC4167418
Subset
IM
Grants
NCRR NIH HHS · R24 RR032341 · United States
NINDS NIH HHS · R01NS076465 · United States
NHGRI NIH HHS · R01HG006798 · United States
NINDS NIH HHS · R01 NS076465 · United States
NCRR NIH HHS · R24RR032341 · United States
NIH HHS · R24 OD011172 · United States
NCI NIH HHS · U10 CA180827 · United States
Databases
GEO
GSE46876
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1038/nbt.2972 PMC Full Text View journal details
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