Abstract

Accuracy, Reproducibility and Consequences of Bias in Quantitative Small RNA-seq For Circulating Cell-free RNA Profiling

Maria Giraldez, Researcher, University of Michigan

Small RNA-seq is increasingly being used for profiling of small RNAs, including cell-free RNA such as microRNAs present in plasma and other biofluids. In practice, small RNAseq can involve many different methods for library preparation, with distinct protocols and technical variations that could cause substantial differences in results, yet these have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters with randomized end-nucleotides for ligation. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide a foundation for reproducible, cross-laboratory small RNAseq studies of cell-free, circulating RNA in a variety of clinical contexts.