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

TitleReproducibility of high-throughput mRNA and small RNA sequencing across laboratories
Publication TypeJournal Article
Year of Publication2013
Authors't Hoen PA, Friedl, Alml, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Br, Consortium TGEUVADIS, van Ommen GJ, Estivill X, Guig, Syv, Gut IG, Dermitzakis ET, Antonorakis SE, Brazma A, Flicek P, Schreiber S, Rosenstiel P, Meitinger T, Strom TM, Lehrach H, Sudbrak R, Carracedo A, 't Hoen PA, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, van Iterson M, Friedl, Monlong J, Lizano E, Bertier G, Ferreira PG, Sammeth M, Alml, Karlberg O, Br, Ribeca P, Griebel T, Beltran S, Gut M, Kahlem K, Lappalainen T, Giger T, Ongen H, Padioleau I, Kilpinen H, Gonz, Kurbatova N, Tikhonov A, Greger L, Barann M, Esser D, H, Wieland T, Schwarzmayr T, Sultan M, Amstislavskiy V, den Dunnen JT, van Ommen GJ, Gut IG, Guig, Estivill X, Syv, Dermitzakis ET, Lappalainen T
JournalNat. Biotechnol.
Date PublishedSep

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.