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Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling

Nature Biotechnology volume 36, pages 746–757 (2018)Cite this article

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An Erratum to this article was published on 01 October 2018

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Abstract

RNA-seq is increasingly used for quantitative profiling of small RNAs (for example, microRNAs, piRNAs and snoRNAs) in diverse sample types, including isolated cells, tissues and cell-free biofluids. The accuracy and reproducibility of the currently used small RNA-seq library preparation methods have not been systematically tested. Here we report results obtained by a consortium of nine labs that independently sequenced reference, 'ground truth' samples of synthetic small RNAs and human plasma-derived RNA. We assessed three commercially available library preparation methods that use adapters of defined sequence and six methods using adapters with degenerate bases. Both protocol- and sequence-specific biases were identified, including biases that reduced the ability of small RNA-seq to accurately measure adenosine-to-inosine editing in microRNAs. We found that these biases were mitigated by library preparation methods that incorporate adapters with degenerate bases. MicroRNA relative quantification between samples using small RNA-seq was accurate and reproducible across laboratories and methods.

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Figure 1: Overview of study design.
Figure 2: Equimolar pool sequencing results across multiple labs and protocols.
Figure 3: Small RNA-seq accuracy and cross-protocol concordance in measuring relative expression levels between samples.
Figure 4: Reproducibility of small RNA-seq within and between labs.
Figure 5: Small RNA-seq of reference plasma RNA by multiple laboratories using multiple library preparation protocols.
Figure 6: Library protocol performance in measuring miRNA A-to-I editing events.

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  • 31 July 2018

    In the version of this article initially published online, the text "Beth Israel Deaconess Medical Center/Dana Farber Cancer Institute (BIDMC/ DFCI)" was inserted into the last sentence in the right-hand column of p.10, beginning "It is worth noting...." . In addition, on p.2, the acronym for The Cancer Genome Atlas was given as TGCA, rather than TCGA; and on p. 3, UUTR should have been defined, as University of Utrecht, the Netherlands. Finally, ref. 48 was cited in the Online Methods after "4N_Xu protocol was performed as previously described35"; this extra citation has been deleted. The errors have been corrected for the print, PDF and HTML versions of this article.

  • 01 October 2018

    Nat. Biotechnol. 10.1038/nbt.4183; corrected online 31 July 2018 In the version of this article initially published online, the text “Beth Israel Deaconess Medical Center/Dana Farber Cancer Institute (BIDMC/DFCI)” was inserted into the last sentence in the right-hand column of p.10, beginning “It isworth noting.

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Acknowledgements

We are grateful to J.S. Rozowsky, R. Kitchen, S.L. Subramanian, W. Thistlethwaite, M.B. Gerstein, A. Milosavljevic and N. Sakhanenko for facilitating access to the exceRpt pipeline and helpful conversations and suggestions. We are also grateful to P.A.C. 't Hoen for helpful discussions. We acknowledge funding support from the NIH Extracellular RNA Communication Common Fund grants: U01 grants HL126499 to M.T., HL126496 to D.J.G. and K.W., HL126493 to D.J.E. and P.G.W., HL126494 to L.C.L., HL126495 to J.E.F., HL126497 to I.G., and UH3 grant TR000891 to K.V.K.-J. M.D.G. acknowledges initial support from a Rio Hortega Fellowship (CM10/00084) and later from a Martin Escudero Fellowship. E.N.M.N.-`t.H. and T.A.P.D. received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement number 337581 and from the Netherlands Organization for Scientific Research (NWO Enabling Technologies project nr 435002022). Y.E.W. received funding from the Dana-Farber Strategic Plan Initiative. K.W. received funding from DOD (W911NF-10-2-0111) and DTRA (HDTRA1-13-C-0055). Research reported in this publication was also supported by the National Cancer Institute of the NIH under Award Number P30CA046592 by the use of the following Cancer Center Shared Resource at the University of Michigan: DNA Sequencing. D.J.G. also acknowledges a special technology support award from the Pacific Northwest Research Institute to his lab. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Author information

Author notes

  1. Maria D Giraldez and Ryan M Spengler: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, Michigan, USA

    Maria D Giraldez, Ryan M Spengler & Muneesh Tewari

  2. Pacific Northwest Research Institute, Seattle, Washington, USA

    Alton Etheridge & David J Galas

  3. Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California, USA

    Paula M Godoy, Andrea J Barczak & David J Erle

  4. Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California, USA.,

    Srimeenakshi Srinivasan, Peter L De Hoff & Louise C Laurent

  5. Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Kahraman Tanriverdi & Jane E Freedman

  6. Neurogenomics, The Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA

    Amanda Courtright & Kendall Van Keuren-Jensen

  7. Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA

    Shulin Lu, Joseph Khoory & Ionita Ghiran

  8. Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Renee Rubio & Yaoyu E Wang

  9. Institute for Systems Biology, Seattle, Washington, USA

    David Baxter & Kai Wang

  10. Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands

    Tom A P Driedonks & Esther N M Nolte-'t Hoen

  11. Department of Human Genetics, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, the Netherlands

    Henk P J Buermans

  12. Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA

    Hui Jiang & Muneesh Tewari

  13. Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA

    Hui Jiang

  14. Cardiovascular Research Institute and the Department of Medicine, Division of Pulmonary, Critical Care, Sleep, and Allergy, University of California San Francisco, San Francisco, California, USA

    Prescott G Woodruff

  15. Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA

    Muneesh Tewari

  16. Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA

    Muneesh Tewari

Authors
  1. Maria D Giraldez
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  2. Ryan M Spengler
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  3. Alton Etheridge
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Contributions

M.D.G. designed, led and coordinated the overall study. This comprised contributions throughout the entire process, including designing, preparing and distributing synthetic RNA pools, creating detailed instructions for the participating labs, performing experiments, coordinating experimental work and communication across labs, and organizing and managing all aspects of the project. In addition, she interpreted study results and was the primary writer of the manuscript. R.M.S. led the computational analyses and data management for this study, including processing data, designing and performing data analyses, identifying and applying methods to visualize data and results, and coordinating data and metadata incoming from collaborating laboratories. He also designed the composition of the ratiometric pools, interpreted results and contributed to the manuscript by preparing the figures, drafting figure legends and writing the computational methods. A.E. contributed to experimental design and preparation of synthetic RNA pools. He also performed experimental work, interpreted results and provided comments on the manuscript. He also developed and contributed the core in-house 4N protocol, variations of which were then used by multiple laboratories. M.T., D.J.G. and D.J.E. helped to design the study and interpret the results, along with contributions from the rest of the study team, including L.C.L., P.G.W., K.V.K.-J., I.G., Y.E.W., K.W., J.E.F., H.J., E.N.M.N.-`t.H. and H.P. J.B. contributed to design of statistical analyses and data interpretation. P.M.G., A.J.B., S.S., P.L.D.H., K.T., A.C., S.L., J.K., R.R., D.B. and T.A.P.D. carried out experiments. M.T. and D.J.G. supervised the overall study and did primary editing of the manuscript with substantial input from D.J.E. All of the authors contributed to reviewing, editing and/or providing comments on the manuscript.

Corresponding authors

Correspondence to Maria D Giraldez, David J Galas or Muneesh Tewari.

Ethics declarations

Competing interests

The spouse of L.C. Laurent is an employee of Illumina, Inc., the manufacturer of the TruSeq Small RNA Library Preparation Kit. L.C. Laurent and her spouse's equity interest in Illumina, Inc. represents <<1% of the company. The other authors declare no competing financial interests.

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Giraldez, M., Spengler, R., Etheridge, A. et al. Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. Nat Biotechnol 36, 746–757 (2018). https://doi.org/10.1038/nbt.4183

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