Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories - PubMed (original) (raw)

. 2013 Nov;31(11):1015-22.

doi: 10.1038/nbt.2702. Epub 2013 Sep 15.

Marc R Friedländer, Jonas Almlöf, Michael Sammeth, Irina Pulyakhina, Seyed Yahya Anvar, Jeroen F J Laros, Henk P J Buermans, Olof Karlberg, Mathias Brännvall; GEUVADIS Consortium; Johan T den Dunnen, Gert-Jan B van Ommen, Ivo G Gut, Roderic Guigó, Xavier Estivill, Ann-Christine Syvänen, Emmanouil T Dermitzakis, Tuuli Lappalainen

Collaborators, Affiliations

• PMID: 24037425
• DOI: 10.1038/nbt.2702

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

Peter A C 't Hoen et al. Nat Biotechnol. 2013 Nov.

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.

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