Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

Peter A C T'Hoen, Marc R. Friedländer, Jonas Almlöf, Michael Sammeth, Irina Pulyakhina, Seyed Yahya Anvar, Jeroen F J Laros, Henk P J Buermans, Olof Karlberg, Mathias Brännvall, Johan T. Den Dunnen, Gert Jan B Van Ommen, Ivo G. Gut, Roderic Guigó, Xavier P. Estivill, Ann Christine Syvänen, Emmanouil T. Dermitzakis, Tuuli Lappalainen

Research output: Contribution to journalArticle

126 Citations (Scopus)

Abstract

RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance. However, understanding of the sources of technical and interlaboratory variation is still limited. To address this, the GEUVADIS consortium sequenced mRNAs and small RNAs of lymphoblastoid cell lines of 465 individuals in seven sequencing centers, with a large number of replicates. The variation between laboratories appeared to be considerably smaller than the already limited biological variation. Laboratory effects were mainly seen in differences in insert size and GC content and could be adequately corrected for. In small-RNA sequencing, the microRNA (miRNA) content differed widely between samples owing to competitive sequencing of rRNA fragments. This did not affect relative quantification of miRNAs. We conclude that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures. We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data.

Original languageEnglish
Pages (from-to)1015-1022
Number of pages8
JournalNature Biotechnology
Volume31
Issue number11
DOIs
Publication statusPublished - Nov 2013
Externally publishedYes

Fingerprint

RNA Sequence Analysis
RNA
Throughput
MicroRNAs
Messenger RNA
Base Composition
Random Allocation
Sequence Analysis
Genome
Guidelines
Technology
Cell Line
Standardization
Genes
Cells

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Biomedical Engineering
  • Molecular Medicine

Cite this

T'Hoen, P. A. C., Friedländer, M. R., Almlöf, J., Sammeth, M., Pulyakhina, I., Anvar, S. Y., ... Lappalainen, T. (2013). Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nature Biotechnology, 31(11), 1015-1022. https://doi.org/10.1038/nbt.2702

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. / T'Hoen, Peter A C; Friedländer, Marc R.; Almlöf, Jonas; Sammeth, Michael; Pulyakhina, Irina; Anvar, Seyed Yahya; Laros, Jeroen F J; Buermans, Henk P J; Karlberg, Olof; Brännvall, Mathias; Den Dunnen, Johan T.; Van Ommen, Gert Jan B; Gut, Ivo G.; Guigó, Roderic; Estivill, Xavier P.; Syvänen, Ann Christine; Dermitzakis, Emmanouil T.; Lappalainen, Tuuli.

In: Nature Biotechnology, Vol. 31, No. 11, 11.2013, p. 1015-1022.

Research output: Contribution to journalArticle

T'Hoen, PAC, Friedländer, MR, Almlöf, J, Sammeth, M, Pulyakhina, I, Anvar, SY, Laros, JFJ, Buermans, HPJ, Karlberg, O, Brännvall, M, Den Dunnen, JT, Van Ommen, GJB, Gut, IG, Guigó, R, Estivill, XP, Syvänen, AC, Dermitzakis, ET & Lappalainen, T 2013, 'Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories', Nature Biotechnology, vol. 31, no. 11, pp. 1015-1022. https://doi.org/10.1038/nbt.2702
T'Hoen PAC, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nature Biotechnology. 2013 Nov;31(11):1015-1022. https://doi.org/10.1038/nbt.2702
T'Hoen, Peter A C ; Friedländer, Marc R. ; Almlöf, Jonas ; Sammeth, Michael ; Pulyakhina, Irina ; Anvar, Seyed Yahya ; Laros, Jeroen F J ; Buermans, Henk P J ; Karlberg, Olof ; Brännvall, Mathias ; Den Dunnen, Johan T. ; Van Ommen, Gert Jan B ; Gut, Ivo G. ; Guigó, Roderic ; Estivill, Xavier P. ; Syvänen, Ann Christine ; Dermitzakis, Emmanouil T. ; Lappalainen, Tuuli. / Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. In: Nature Biotechnology. 2013 ; Vol. 31, No. 11. pp. 1015-1022.
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