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A framework for RNA quality correction in differential expression analysis

Andrew E. Jaffe, Ran Tao, Alexis L. Norris, Marc Kealhofer, Abhinav Nellore, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Richard E. Straub, Jeffrey T. Leek, Daniel R. Weinberger
doi: https://doi.org/10.1101/074245
Andrew E. Jaffe
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
2Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
3Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
4Center for Computational Biology, Johns Hopkins University, Baltimore MD 21205 USA
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Ran Tao
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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Alexis L. Norris
5Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
6Department of Neurology, Kennedy Krieger Institute, Baltimore, MD 21205 USA
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Marc Kealhofer
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
7Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
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Abhinav Nellore
3Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
4Center for Computational Biology, Johns Hopkins University, Baltimore MD 21205 USA
8Department of Computer Science, Johns Hopkins University, Baltimore MD 21205 USA
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Yankai Jia
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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Thomas M. Hyde
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
9Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
10Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Joel E. Kleinman
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
10Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Richard E. Straub
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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Jeffrey T. Leek
3Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
4Center for Computational Biology, Johns Hopkins University, Baltimore MD 21205 USA
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Daniel R. Weinberger
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
10Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
11Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
12McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Abstract

RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. We demonstrate here that statistical adjustment employing existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from a molecular degradation experiment of human brain tissue, we introduce the quality surrogate variable (qSVA) analysis framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. We show this approach results in greatly improved replication rates (>3x) across two large independent postmortem human brain studies of schizophrenia. Finally, we explored public datasets to demonstrate potential RNA quality confounding when comparing expression levels of different brain regions and diagnostic groups beyond schizophrenia. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from the human brain.

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Posted September 09, 2016.
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A framework for RNA quality correction in differential expression analysis
Andrew E. Jaffe, Ran Tao, Alexis L. Norris, Marc Kealhofer, Abhinav Nellore, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Richard E. Straub, Jeffrey T. Leek, Daniel R. Weinberger
bioRxiv 074245; doi: https://doi.org/10.1101/074245
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A framework for RNA quality correction in differential expression analysis
Andrew E. Jaffe, Ran Tao, Alexis L. Norris, Marc Kealhofer, Abhinav Nellore, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Richard E. Straub, Jeffrey T. Leek, Daniel R. Weinberger
bioRxiv 074245; doi: https://doi.org/10.1101/074245

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