Comprehensive multi-center assessment of accuracy, reproducibility and bias of small RNA-seq methods for quantitative miRNA profiling

Autor: Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-‘t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, Tewari, M
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Zdroj: Nature biotechnology
ISSN: 1546-1696
1087-0156
Popis: RNA-seq is increasingly employed for quantitative profiling of small RNAs (e.g., microRNAs, piRNAs, snoRNAs) in diverse sample types including isolated cells, tissues and cell-free biofluids. The accuracy and reproducibility of the multiple small RNA-seq library preparation methods in use, however, have not been systematically assessed. We report systematic results obtained by a consortium of nine labs that independently sequenced reference, ‘ground truth’, samples of synthetic small RNAs and human plasma-derived RNA. Three commercially available library preparation methods employing adapters of defined sequence and six methods using adapters with degenerate bases were assessed. Both protocol- and sequence-specific biases were identified, including biases that reduce the ability of small RNA-seq to accurately measure adenosine-to-inosine editing in microRNAs. We report 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 found to be accurate and reproducible across laboratories and methods.
Databáze: OpenAIRE
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